├── LICENSE ├── README.md ├── img └── FIG1.png ├── parse_motifs ├── Makefile ├── jaspar │ └── jaspar_raw │ │ ├── MA0001.1.pfm │ │ ├── MA0002.2.pfm │ │ ├── MA0003.1.pfm │ │ ├── MA0004.1.pfm │ │ ├── MA0005.1.pfm │ │ ├── MA0006.1.pfm │ │ ├── MA0007.1.pfm │ │ ├── MA0008.1.pfm │ │ ├── MA0009.1.pfm │ │ ├── MA0010.1.pfm │ │ ├── MA0011.1.pfm │ │ ├── MA0012.1.pfm │ │ ├── MA0013.1.pfm │ │ ├── MA0014.1.pfm │ │ ├── MA0015.1.pfm │ │ ├── MA0016.1.pfm │ │ ├── MA0017.1.pfm │ │ ├── MA0018.2.pfm │ │ ├── MA0019.1.pfm │ │ ├── MA0020.1.pfm │ │ ├── MA0021.1.pfm │ │ ├── MA0022.1.pfm │ │ ├── MA0023.1.pfm │ │ ├── MA0024.1.pfm │ │ ├── MA0025.1.pfm │ │ ├── MA0026.1.pfm │ │ ├── MA0027.1.pfm │ │ ├── MA0028.1.pfm │ │ ├── MA0029.1.pfm │ │ ├── MA0030.1.pfm │ │ ├── MA0031.1.pfm │ │ ├── MA0032.1.pfm │ │ ├── MA0033.1.pfm │ │ ├── MA0034.1.pfm │ │ ├── MA0035.2.pfm │ │ ├── MA0036.1.pfm │ │ ├── MA0037.1.pfm │ │ ├── MA0038.1.pfm │ │ ├── MA0039.2.pfm │ │ ├── MA0040.1.pfm │ │ ├── MA0041.1.pfm │ │ ├── MA0042.1.pfm │ │ ├── MA0043.1.pfm │ │ ├── MA0044.1.pfm │ │ ├── MA00445.1.pfm │ │ ├── MA0045.1.pfm │ │ ├── MA0046.1.pfm │ │ ├── MA0047.2.pfm │ │ ├── MA0048.1.pfm │ │ ├── MA0049.1.pfm │ │ ├── MA0050.1.pfm │ │ ├── MA0051.1.pfm │ │ ├── MA0052.1.pfm │ │ ├── MA0053.1.pfm │ │ ├── MA0054.1.pfm │ │ ├── MA0055.1.pfm │ │ ├── MA0056.1.pfm │ │ ├── MA0057.1.pfm │ │ ├── MA0058.1.pfm │ │ ├── MA0059.1.pfm │ │ ├── MA0060.1.pfm │ │ ├── MA0061.1.pfm │ │ ├── MA0062.2.pfm │ │ ├── MA0063.1.pfm │ │ ├── MA0064.1.pfm │ │ ├── MA0065.2.pfm │ │ ├── MA0066.1.pfm │ │ ├── MA0067.1.pfm │ │ ├── MA0068.1.pfm │ │ ├── MA0069.1.pfm │ │ ├── MA0070.1.pfm │ │ ├── MA0071.1.pfm │ │ ├── MA0072.1.pfm │ │ ├── MA0073.1.pfm │ │ ├── MA0074.1.pfm │ │ ├── MA0075.1.pfm │ │ ├── MA0076.1.pfm │ │ ├── MA0077.1.pfm │ │ ├── MA0078.1.pfm │ │ ├── MA0079.2.pfm │ │ ├── MA0080.2.pfm │ │ ├── MA0081.1.pfm │ │ ├── MA0082.1.pfm │ │ ├── MA0083.1.pfm │ │ ├── MA0084.1.pfm │ │ ├── MA0085.1.pfm │ │ ├── MA0086.1.pfm │ │ ├── MA0087.1.pfm │ │ ├── MA0088.1.pfm │ │ ├── MA0089.1.pfm │ │ ├── MA0090.1.pfm │ │ ├── MA0091.1.pfm │ │ ├── MA0092.1.pfm │ │ ├── MA0093.1.pfm │ │ ├── MA0094.2.pfm │ │ ├── MA0095.1.pfm │ │ ├── MA0096.1.pfm │ │ ├── MA0097.1.pfm │ │ ├── MA0098.1.pfm │ │ ├── MA0099.2.pfm │ │ ├── MA0100.1.pfm │ │ ├── MA0101.1.pfm │ │ ├── MA0102.2.pfm │ │ ├── MA0103.1.pfm │ │ ├── MA0104.2.pfm │ │ ├── MA0105.1.pfm │ │ ├── MA0106.1.pfm │ │ ├── MA0107.1.pfm │ │ ├── MA0108.2.pfm │ │ ├── MA0109.1.pfm │ │ ├── MA0110.1.pfm │ │ ├── MA0111.1.pfm │ │ ├── MA0112.2.pfm │ │ ├── MA0113.1.pfm │ │ ├── MA0114.1.pfm │ │ ├── MA0115.1.pfm │ │ ├── MA0116.1.pfm │ │ ├── MA0117.1.pfm │ │ ├── MA0118.1.pfm │ │ ├── MA0119.1.pfm │ │ ├── MA0120.1.pfm │ │ ├── MA0121.1.pfm │ │ ├── MA0122.1.pfm │ │ ├── MA0123.1.pfm │ │ ├── MA0124.1.pfm │ │ ├── MA0125.1.pfm │ │ ├── MA0126.1.pfm │ │ ├── MA0127.1.pfm │ │ ├── MA0128.1.pfm │ │ ├── MA0129.1.pfm │ │ ├── MA0130.1.pfm │ │ ├── MA0131.1.pfm │ │ ├── MA0132.1.pfm │ │ ├── MA0133.1.pfm │ │ ├── MA0135.1.pfm │ │ ├── MA0136.1.pfm │ │ ├── MA0137.2.pfm │ │ ├── MA0138.2.pfm │ │ ├── MA0139.1.pfm │ │ ├── MA0140.1.pfm │ │ ├── MA0141.1.pfm │ │ ├── MA0142.1.pfm │ │ ├── MA0143.1.pfm │ │ ├── MA0144.1.pfm │ │ ├── MA0145.1.pfm │ │ ├── MA0146.1.pfm │ │ ├── MA0147.1.pfm │ │ ├── MA0148.1.pfm │ │ ├── MA0149.1.pfm │ │ ├── MA0150.1.pfm │ │ ├── MA0151.1.pfm │ │ ├── MA0152.1.pfm │ │ ├── MA0153.1.pfm │ │ ├── MA0154.1.pfm │ │ ├── MA0155.1.pfm │ │ ├── MA0156.1.pfm │ │ ├── MA0157.1.pfm │ │ ├── MA0158.1.pfm │ │ ├── MA0159.1.pfm │ │ ├── MA0160.1.pfm │ │ ├── MA0161.1.pfm │ │ ├── MA0162.1.pfm │ │ ├── MA0163.1.pfm │ │ ├── MA0164.1.pfm │ │ ├── MA0165.1.pfm │ │ ├── MA0166.1.pfm │ │ ├── MA0167.1.pfm │ │ ├── MA0168.1.pfm │ │ ├── MA0169.1.pfm │ │ ├── MA0170.1.pfm │ │ ├── MA0171.1.pfm │ │ ├── MA0172.1.pfm │ │ ├── MA0173.1.pfm │ │ ├── MA0174.1.pfm │ │ ├── MA0175.1.pfm │ │ ├── MA0176.1.pfm │ │ ├── MA0177.1.pfm │ │ ├── MA0178.1.pfm │ │ ├── MA0179.1.pfm │ │ ├── MA0180.1.pfm │ │ ├── MA0181.1.pfm │ │ ├── MA0182.1.pfm │ │ ├── MA0183.1.pfm │ │ ├── MA0184.1.pfm │ │ ├── MA0185.1.pfm │ │ ├── MA0186.1.pfm │ │ ├── MA0187.1.pfm │ │ ├── MA0188.1.pfm │ │ ├── MA0189.1.pfm │ │ ├── MA0190.1.pfm │ │ ├── MA0191.1.pfm │ │ ├── MA0192.1.pfm │ │ ├── MA0193.1.pfm │ │ ├── MA0194.1.pfm │ │ ├── MA0195.1.pfm │ │ ├── MA0196.1.pfm │ │ ├── MA0197.1.pfm │ │ ├── MA0198.1.pfm │ │ ├── MA0199.1.pfm │ │ ├── MA0200.1.pfm │ │ ├── MA0201.1.pfm │ │ ├── MA0202.1.pfm │ │ ├── MA0203.1.pfm │ │ ├── MA0204.1.pfm │ │ ├── MA0205.1.pfm │ │ ├── MA0206.1.pfm │ │ ├── MA0207.1.pfm │ │ ├── MA0208.1.pfm │ │ ├── MA0209.1.pfm │ │ ├── MA0210.1.pfm │ │ ├── MA0211.1.pfm │ │ ├── MA0212.1.pfm │ │ ├── MA0213.1.pfm │ │ ├── MA0214.1.pfm │ │ ├── MA0215.1.pfm │ │ ├── MA0216.1.pfm │ │ ├── MA0217.1.pfm │ │ ├── MA0218.1.pfm │ │ ├── MA0219.1.pfm │ │ ├── MA0220.1.pfm │ │ ├── MA0221.1.pfm │ │ ├── MA0222.1.pfm │ │ ├── MA0223.1.pfm │ │ ├── MA0224.1.pfm │ │ ├── MA0225.1.pfm │ │ ├── MA0226.1.pfm │ │ ├── MA0227.1.pfm │ │ ├── MA0228.1.pfm │ │ ├── MA0229.1.pfm │ │ ├── MA0230.1.pfm │ │ ├── MA0231.1.pfm │ │ ├── MA0232.1.pfm │ │ ├── MA0233.1.pfm │ │ ├── MA0234.1.pfm │ │ ├── MA0235.1.pfm │ │ ├── MA0236.1.pfm │ │ ├── MA0237.1.pfm │ │ ├── MA0238.1.pfm │ │ ├── MA0239.1.pfm │ │ ├── MA0240.1.pfm │ │ ├── MA0241.1.pfm │ │ ├── MA0242.1.pfm │ │ ├── MA0243.1.pfm │ │ ├── MA0244.1.pfm │ │ ├── MA0245.1.pfm │ │ ├── MA0246.1.pfm │ │ ├── MA0247.1.pfm │ │ ├── MA0248.1.pfm │ │ ├── MA0249.1.pfm │ │ ├── MA0250.1.pfm │ │ ├── MA0251.1.pfm │ │ ├── MA0252.1.pfm │ │ ├── MA0253.1.pfm │ │ ├── MA0254.1.pfm │ │ ├── MA0255.1.pfm │ │ ├── MA0256.1.pfm │ │ ├── MA0257.1.pfm │ │ ├── MA0258.1.pfm │ │ ├── MA0259.1.pfm │ │ ├── MA0260.1.pfm │ │ ├── MA0261.1.pfm │ │ ├── MA0262.1.pfm │ │ ├── MA0263.1.pfm │ │ ├── MA0264.1.pfm │ │ ├── MA0265.1.pfm │ │ ├── MA0266.1.pfm │ │ ├── MA0267.1.pfm │ │ ├── MA0268.1.pfm │ │ ├── MA0269.1.pfm │ │ ├── MA0270.1.pfm │ │ ├── MA0271.1.pfm │ │ ├── MA0272.1.pfm │ │ ├── MA0273.1.pfm │ │ ├── MA0274.1.pfm │ │ ├── MA0275.1.pfm │ │ ├── MA0276.1.pfm │ │ ├── MA0277.1.pfm │ │ ├── MA0278.1.pfm │ │ ├── MA0279.1.pfm │ │ ├── MA0280.1.pfm │ │ ├── MA0281.1.pfm │ │ ├── MA0282.1.pfm │ │ ├── MA0283.1.pfm │ │ ├── MA0284.1.pfm │ │ ├── MA0285.1.pfm │ │ ├── MA0286.1.pfm │ │ ├── MA0287.1.pfm │ │ ├── MA0288.1.pfm │ │ ├── MA0289.1.pfm │ │ ├── MA0290.1.pfm │ │ ├── MA0291.1.pfm │ │ ├── MA0292.1.pfm │ │ ├── MA0293.1.pfm │ │ ├── MA0294.1.pfm │ │ ├── MA0295.1.pfm │ │ ├── MA0296.1.pfm │ │ ├── MA0297.1.pfm │ │ ├── MA0298.1.pfm │ │ ├── MA0299.1.pfm │ │ ├── MA0300.1.pfm │ │ ├── MA0301.1.pfm │ │ ├── MA0302.1.pfm │ │ ├── MA0303.1.pfm │ │ ├── MA0304.1.pfm │ │ ├── MA0305.1.pfm │ │ ├── MA0306.1.pfm │ │ ├── MA0307.1.pfm │ │ ├── MA0308.1.pfm │ │ ├── MA0309.1.pfm │ │ ├── MA0310.1.pfm │ │ ├── MA0311.1.pfm │ │ ├── MA0312.1.pfm │ │ ├── MA0313.1.pfm │ │ ├── MA0314.1.pfm │ │ ├── MA0315.1.pfm │ │ ├── MA0316.1.pfm │ │ ├── MA0317.1.pfm │ │ ├── MA0318.1.pfm │ │ ├── MA0319.1.pfm │ │ ├── MA0320.1.pfm │ │ ├── MA0321.1.pfm │ │ ├── MA0322.1.pfm │ │ ├── MA0323.1.pfm │ │ ├── MA0324.1.pfm │ │ ├── MA0325.1.pfm │ │ ├── MA0326.1.pfm │ │ ├── MA0327.1.pfm │ │ ├── MA0328.1.pfm │ │ ├── MA0329.1.pfm │ │ ├── MA0330.1.pfm │ │ ├── MA0331.1.pfm │ │ ├── MA0332.1.pfm │ │ ├── MA0333.1.pfm │ │ ├── MA0334.1.pfm │ │ ├── MA0335.1.pfm │ │ ├── MA0336.1.pfm │ │ ├── MA0337.1.pfm │ │ ├── MA0338.1.pfm │ │ ├── MA0339.1.pfm │ │ ├── MA0340.1.pfm │ │ ├── MA0341.1.pfm │ │ ├── MA0342.1.pfm │ │ ├── MA0343.1.pfm │ │ ├── MA0344.1.pfm │ │ ├── MA0345.1.pfm │ │ ├── MA0346.1.pfm │ │ ├── MA0347.1.pfm │ │ ├── MA0348.1.pfm │ │ ├── MA0349.1.pfm │ │ ├── MA0350.1.pfm │ │ ├── MA0351.1.pfm │ │ ├── MA0352.1.pfm │ │ ├── MA0353.1.pfm │ │ ├── MA0354.1.pfm │ │ ├── MA0355.1.pfm │ │ ├── MA0356.1.pfm │ │ ├── MA0357.1.pfm │ │ ├── MA0358.1.pfm │ │ ├── MA0359.1.pfm │ │ ├── MA0360.1.pfm │ │ ├── MA0361.1.pfm │ │ ├── MA0362.1.pfm │ │ ├── MA0363.1.pfm │ │ ├── MA0364.1.pfm │ │ ├── MA0365.1.pfm │ │ ├── MA0366.1.pfm │ │ ├── MA0367.1.pfm │ │ ├── MA0368.1.pfm │ │ ├── MA0369.1.pfm │ │ ├── MA0370.1.pfm │ │ ├── MA0371.1.pfm │ │ ├── MA0372.1.pfm │ │ ├── MA0373.1.pfm │ │ ├── MA0374.1.pfm │ │ ├── MA0375.1.pfm │ │ ├── MA0376.1.pfm │ │ ├── MA0377.1.pfm │ │ ├── MA0378.1.pfm │ │ ├── MA0379.1.pfm │ │ ├── MA0380.1.pfm │ │ ├── MA0381.1.pfm │ │ ├── MA0382.1.pfm │ │ ├── MA0383.1.pfm │ │ ├── MA0384.1.pfm │ │ ├── MA0385.1.pfm │ │ ├── MA0386.1.pfm │ │ ├── MA0387.1.pfm │ │ ├── MA0388.1.pfm │ │ ├── MA0389.1.pfm │ │ ├── MA0390.1.pfm │ │ ├── MA0391.1.pfm │ │ ├── MA0392.1.pfm │ │ ├── MA0393.1.pfm │ │ ├── MA0394.1.pfm │ │ ├── MA0395.1.pfm │ │ ├── MA0396.1.pfm │ │ ├── MA0397.1.pfm │ │ ├── MA0398.1.pfm │ │ ├── MA0399.1.pfm │ │ ├── MA0400.1.pfm │ │ ├── MA0401.1.pfm │ │ ├── MA0402.1.pfm │ │ ├── MA0403.1.pfm │ │ ├── MA0404.1.pfm │ │ ├── MA0405.1.pfm │ │ ├── MA0406.1.pfm │ │ ├── MA0407.1.pfm │ │ ├── MA0408.1.pfm │ │ ├── MA0409.1.pfm │ │ ├── MA0410.1.pfm │ │ ├── MA0411.1.pfm │ │ ├── MA0412.1.pfm │ │ ├── MA0413.1.pfm │ │ ├── MA0414.1.pfm │ │ ├── MA0415.1.pfm │ │ ├── MA0416.1.pfm │ │ ├── MA0417.1.pfm │ │ ├── MA0418.1.pfm │ │ ├── MA0419.1.pfm │ │ ├── MA0420.1.pfm │ │ ├── MA0421.1.pfm │ │ ├── MA0422.1.pfm │ │ ├── MA0423.1.pfm │ │ ├── MA0424.1.pfm │ │ ├── MA0425.1.pfm │ │ ├── MA0426.1.pfm │ │ ├── MA0427.1.pfm │ │ ├── MA0428.1.pfm │ │ ├── MA0429.1.pfm │ │ ├── MA0430.1.pfm │ │ ├── MA0431.1.pfm │ │ ├── MA0432.1.pfm │ │ ├── MA0433.1.pfm │ │ ├── MA0434.1.pfm │ │ ├── MA0435.1.pfm │ │ ├── MA0436.1.pfm │ │ ├── MA0437.1.pfm │ │ ├── MA0438.1.pfm │ │ ├── MA0439.1.pfm │ │ ├── MA0440.1.pfm │ │ ├── MA0441.1.pfm │ │ ├── MA0442.1.pfm │ │ ├── MA0443.1.pfm │ │ ├── MA0444.1.pfm │ │ ├── MA0446.1.pfm │ │ ├── MA0447.1.pfm │ │ ├── MA0448.1.pfm │ │ ├── MA0449.1.pfm │ │ ├── MA0450.1.pfm │ │ ├── MA0451.1.pfm │ │ ├── MA0452.1.pfm │ │ ├── MA0453.1.pfm │ │ ├── MA0454.1.pfm │ │ ├── MA0455.1.pfm │ │ ├── MA0456.1.pfm │ │ ├── MA0457.1.pfm │ │ ├── MA0458.1.pfm │ │ ├── MA0459.1.pfm │ │ ├── MA0460.1.pfm │ │ ├── README.txt │ │ ├── makeJASPAR.pl │ │ └── matrix_list.txt ├── jolma │ ├── green.txt │ ├── makeMatrix.pl │ ├── orange.txt │ ├── run.bsh │ └── teal.txt ├── neph │ ├── makeNeph.pl │ ├── neph.txt │ └── readme.txt └── uniprobe │ ├── makeUNIPROBE.pl │ └── readme.txt ├── rtfbsdb-manual.pdf ├── rtfbsdb-tutorial.pptx ├── rtfbsdb-vignette.pdf ├── rtfbsdb ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── clustering.R │ ├── common.R │ ├── comp_sites.R │ ├── create_tfbs.R │ ├── draw_motif.R │ ├── express.R │ ├── import_MotifDb.R │ ├── import_motif.R │ ├── motif.R │ ├── output_report.R │ ├── scan_sites.R │ ├── seqLogo.R │ ├── z_CisBP.R │ ├── z_tfbs.R │ └── zzz.R ├── README.md ├── inst │ └── extdata │ │ ├── Chipseq-k562-chr19-E2F4.bed │ │ ├── Chipseq-k562-chr19-EGR1.bed │ │ ├── Chipseq-k562-chr19-ELF1.bed │ │ ├── Chipseq-k562-chr19-EP300.bed │ │ ├── Chipseq-k562-chr19-ETS1.bed │ │ ├── Drosophila_melanogaster_ver_2015_12_08.zip │ │ ├── GSM1480327_K562_PROseq_chr19_minus.bw │ │ ├── GSM1480327_K562_PROseq_chr19_plus.bw │ │ ├── HOCOMOCO_10_pwms_HUMAN_mono.txt │ │ ├── HOCOMOCO_10_pwms_MOUSE_mono.txt │ │ ├── Homo_sapiens_ver_2015_12_08.zip │ │ ├── M3590_1.01.pwm │ │ ├── M3591_1.01.pwm │ │ ├── Mus_musculus_ver_2015_12_08.zip │ │ ├── chrom_info_hg19.tab │ │ ├── chrom_info_mm10.tab │ │ ├── fake_M2938_1.02.pwm │ │ ├── fake_M2940_1.02.pwm │ │ ├── gencode.v19.annotation.chr19.gtf.gz │ │ ├── hg19.chr19.2bit │ │ ├── human_PI_fastq_gz_sort_chr19.bam │ │ ├── human_PI_fastq_gz_sort_chr19.bam.bai │ │ ├── jaspar-insecta.jaspar │ │ ├── k562.chr19.dnase.UW.DUKE.inters.bed │ │ ├── pwm.example.jaspar.2015.txt │ │ ├── pwm.example.meme.Homo_sapiens.txt │ │ ├── pwm.example.meme.txt │ │ ├── pwm.example.mscan.jaspar2010.txt │ │ ├── pwm.example.nature15518.s1.txt │ │ ├── pwm.example.transfac.txt │ │ ├── pwm.format.jaspar.txt │ │ ├── pwm.format.meme.txt │ │ ├── pwm.format.mscan.txt │ │ └── pwm.format.transfac.txt └── man │ ├── CisBP.db.class.Rd │ ├── CisBP.download.Rd │ ├── CisBP.extdata.Rd │ ├── CisBP.getTFinformation.Rd │ ├── CisBP.group.Rd │ ├── CisBP.zipload.Rd │ ├── print.tfbs.enrichment.Rd │ ├── print.tfbs.finding.Rd │ ├── summary.tfbs.enrichment.Rd │ ├── summary.tfbs.finding.Rd │ ├── tfbs.Rd │ ├── tfbs.class.Rd │ ├── tfbs.clusterMotifs.Rd │ ├── tfbs.createFromCisBP.Rd │ ├── tfbs.createFromMotifDb.Rd │ ├── tfbs.db.class.Rd │ ├── tfbs.dirs.Rd │ ├── tfbs.drawLogo.Rd │ ├── tfbs.drawLogosForClusters.Rd │ ├── tfbs.enrichmentTest.Rd │ ├── tfbs.getDistanceMatrix.Rdxx │ ├── tfbs.getExpression.Rd │ ├── tfbs.importMotifs.Rd │ ├── tfbs.plotEnrichment.Rd │ ├── tfbs.reportEnrichment.Rd │ ├── tfbs.reportFinding.Rd │ ├── tfbs.scanTFsite.Rd │ ├── tfbs.selectByGeneExp.Rd │ ├── tfbs.selectByRandom.Rd │ └── tfbs.selectExpressedMotifs.Rd └── test ├── cisbp.test.R ├── dog.export.R ├── hg19.exportTF.R ├── horse.export.R ├── mm10.export.R ├── motif_intersected_sorted_uniq_sortedByAbsLogRatio.rdata ├── rtfbs.plotEnrichment.test.R ├── tfbs.G1.scan.R ├── tfbs.comp.R ├── tfbs.comp.bat ├── tfbs.comp.full.R ├── tfbs.createFromCisBP.R ├── tfbs.dirs.test.R ├── tfbs.drawLogo.R ├── tfbs.importMotifs.R ├── tfbs.scan.R ├── tfbs.scan.bat ├── tfbs.test.R └── tfbs.test.bat /img/FIG1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/img/FIG1.png -------------------------------------------------------------------------------- /parse_motifs/Makefile: -------------------------------------------------------------------------------- 1 | make_all: 2 | cd jaspar/jaspar_raw 3 | bash README.txt 4 | cd ../../neph 5 | bash readme.txt 6 | cd ../jolma 7 | bash run.bsh 8 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0001.1.pfm: -------------------------------------------------------------------------------- 1 | 0 3 79 40 66 48 65 11 65 0 2 | 94 75 4 3 1 2 5 2 3 3 3 | 1 0 3 4 1 0 5 3 28 88 4 | 2 19 11 50 29 47 22 81 1 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0002.2.pfm: -------------------------------------------------------------------------------- 1 | 287 234 123 57 0 87 0 17 10 131 500 2 | 496 485 1072 0 75 127 0 42 400 463 158 3 | 696 467 149 7 1872 70 1987 1848 251 81 289 4 | 521 814 656 1936 53 1716 13 93 1339 1325 1053 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0003.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 22 19 55 53 19 9 2 | 0 185 185 71 57 44 30 16 78 3 | 185 0 0 46 61 67 91 137 79 4 | 0 0 0 46 48 19 11 13 19 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0004.1.pfm: -------------------------------------------------------------------------------- 1 | 4 19 0 0 0 0 2 | 16 0 20 0 0 0 3 | 0 1 0 20 0 20 4 | 0 0 0 0 20 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0005.1.pfm: -------------------------------------------------------------------------------- 1 | 0 2 38 61 73 31 23 20 22 1 27 2 | 87 86 9 5 1 3 16 13 0 0 25 3 | 2 0 7 2 1 4 17 26 64 82 9 4 | 1 2 36 22 15 52 34 31 4 7 29 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0006.1.pfm: -------------------------------------------------------------------------------- 1 | 3 0 0 0 0 0 2 | 8 0 23 0 0 0 3 | 2 23 0 23 0 24 4 | 11 1 1 1 24 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0007.1.pfm: -------------------------------------------------------------------------------- 1 | 9 9 11 16 0 12 21 0 15 4 5 6 3 0 4 11 1 3 6 6 10 5 2 | 7 2 3 1 0 6 2 24 0 9 11 9 5 0 0 5 22 16 7 5 11 11 3 | 2 3 3 7 22 1 0 0 8 2 2 9 1 24 0 1 1 1 5 9 0 6 4 | 6 10 7 0 2 5 1 0 1 9 6 0 15 0 20 7 0 4 6 4 3 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0008.1.pfm: -------------------------------------------------------------------------------- 1 | 3 21 25 0 0 24 1 0 2 | 13 1 0 0 5 0 0 0 3 | 4 0 0 0 0 1 0 2 4 | 5 3 0 25 20 0 24 23 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0009.1.pfm: -------------------------------------------------------------------------------- 1 | 2 1 40 0 0 0 0 0 1 40 31 2 | 28 1 0 0 0 0 0 2 7 0 5 3 | 8 0 0 40 40 0 40 0 28 0 0 4 | 2 38 0 0 0 40 0 38 4 0 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0010.1.pfm: -------------------------------------------------------------------------------- 1 | 3 1 5 7 3 6 4 7 1 9 8 5 4 2 2 | 1 1 2 0 0 0 1 0 8 0 0 0 0 3 3 | 4 1 1 1 0 0 4 1 0 0 1 3 0 2 4 | 1 6 1 1 6 3 0 1 0 0 0 1 5 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0011.1.pfm: -------------------------------------------------------------------------------- 1 | 3 5 0 0 12 1 2 1 2 | 1 2 10 1 0 1 0 2 3 | 1 1 0 0 0 2 1 1 4 | 7 4 2 11 0 8 9 8 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0012.1.pfm: -------------------------------------------------------------------------------- 1 | 3 9 10 12 0 4 10 6 6 4 2 2 | 1 2 0 0 10 0 0 0 1 3 3 3 | 1 1 0 0 1 0 0 4 2 2 5 4 | 7 0 2 0 1 8 2 2 3 3 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0013.1.pfm: -------------------------------------------------------------------------------- 1 | 1 4 2 1 5 6 5 1 3 5 3 2 | 1 0 0 0 0 0 0 3 0 0 1 3 | 0 0 4 0 1 0 1 1 1 0 0 4 | 4 2 0 5 0 0 0 1 2 1 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0014.1.pfm: -------------------------------------------------------------------------------- 1 | 4 4 4 1 2 7 2 0 1 6 6 0 2 3 1 6 5 2 2 5 2 | 1 0 3 2 7 2 5 3 2 1 0 0 8 0 0 1 1 10 5 0 3 | 4 8 3 5 1 1 3 2 8 3 2 12 1 9 4 5 5 0 5 6 4 | 3 0 2 4 2 2 2 7 1 2 4 0 1 0 7 0 1 0 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0015.1.pfm: -------------------------------------------------------------------------------- 1 | 25 1 74 0 78 1 41 2 53 12 2 | 13 2 2 9 2 4 2 9 3 29 3 | 40 1 4 4 0 1 36 1 20 15 4 | 2 76 0 67 0 74 1 68 4 24 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0016.1.pfm: -------------------------------------------------------------------------------- 1 | 0 1 0 0 0 0 35 5 5 6 2 | 1 0 0 0 0 36 0 25 8 10 3 | 37 36 38 38 0 1 3 3 22 16 4 | 0 1 0 0 38 1 0 5 3 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0017.1.pfm: -------------------------------------------------------------------------------- 1 | 0 1 12 6 0 0 0 1 2 6 6 1 3 0 2 | 0 0 0 7 13 3 2 0 0 4 5 10 6 3 3 | 2 12 1 0 0 0 0 0 11 3 1 1 0 3 4 | 11 0 0 0 0 10 11 12 0 0 1 1 4 7 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0018.2.pfm: -------------------------------------------------------------------------------- 1 | 0 0 11 0 1 0 2 8 2 | 1 1 0 9 0 3 7 0 3 | 1 10 0 2 10 0 1 1 4 | 9 0 0 0 0 8 1 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0019.1.pfm: -------------------------------------------------------------------------------- 1 | 14 11 18 0 0 4 38 36 0 14 4 0 2 | 7 7 3 1 0 33 1 2 6 17 23 26 3 | 12 14 15 0 38 0 0 1 0 5 9 6 4 | 6 7 3 38 1 2 0 0 33 3 3 7 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0020.1.pfm: -------------------------------------------------------------------------------- 1 | 21 21 21 0 3 7 2 | 0 0 0 0 14 6 3 | 0 0 0 21 2 3 4 | 0 0 0 0 2 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0021.1.pfm: -------------------------------------------------------------------------------- 1 | 21 21 21 0 0 6 2 | 0 0 0 0 10 6 3 | 0 0 0 21 3 9 4 | 0 0 0 0 8 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0022.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 1 1 1 0 0 1 1 3 2 | 5 0 1 0 1 0 0 0 3 9 9 5 3 | 6 12 11 10 3 2 0 0 0 0 1 5 4 | 2 1 1 3 8 10 12 13 10 3 2 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0023.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 4 2 0 0 0 1 2 | 1 0 0 0 1 1 0 1 9 8 3 | 7 7 9 8 0 0 0 0 0 0 4 | 1 2 0 1 4 6 9 8 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0024.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 0 0 0 0 2 | 0 0 0 4 2 10 0 9 3 | 0 0 0 6 8 0 10 1 4 | 10 10 10 0 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0025.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 22 0 2 0 23 22 0 7 5 2 | 0 0 0 8 0 0 0 0 11 5 5 3 | 0 2 0 0 21 0 0 1 4 7 3 4 | 22 21 1 15 0 23 0 0 8 4 10 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0026.1.pfm: -------------------------------------------------------------------------------- 1 | 2 5 0 0 17 17 5 2 | 12 12 0 0 0 0 1 3 | 2 0 17 17 0 0 10 4 | 1 0 0 0 0 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0027.1.pfm: -------------------------------------------------------------------------------- 1 | 4 5 3 0 4 3 3 2 1 1 1 2 | 1 2 0 0 0 0 0 1 3 4 6 3 | 2 2 7 2 3 7 0 4 3 1 1 4 | 3 1 0 8 3 0 7 3 3 4 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0028.1.pfm: -------------------------------------------------------------------------------- 1 | 7 10 9 5 2 0 1 27 21 13 2 | 7 6 4 19 24 0 0 0 5 0 3 | 10 6 10 1 1 24 27 1 0 14 4 | 4 6 5 3 1 4 0 0 2 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0029.1.pfm: -------------------------------------------------------------------------------- 1 | 14 20 0 27 1 27 26 0 27 0 24 23 6 15 2 | 2 1 1 0 10 0 0 0 0 3 1 0 7 6 3 | 6 2 25 0 0 0 1 27 0 0 0 4 7 3 4 | 5 4 1 0 16 0 0 0 0 24 2 0 7 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0030.1.pfm: -------------------------------------------------------------------------------- 1 | 1 10 17 13 3 7 0 27 27 27 0 27 16 7 2 | 10 7 4 5 11 0 0 0 0 0 25 0 4 4 3 | 7 5 2 5 8 20 0 0 0 0 0 0 2 6 4 | 9 5 4 5 0 0 27 0 0 0 2 0 5 10 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0031.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 19 20 18 1 20 7 2 | 1 0 1 0 1 18 0 2 3 | 17 0 0 0 1 0 0 3 4 | 1 20 0 0 0 1 0 8 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0032.1.pfm: -------------------------------------------------------------------------------- 1 | 4 2 4 6 7 0 0 16 2 | 4 5 4 4 3 0 0 0 3 | 5 6 3 5 2 16 0 0 4 | 3 3 5 1 4 0 16 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0033.1.pfm: -------------------------------------------------------------------------------- 1 | 7 10 6 13 4 21 0 22 2 | 1 4 3 4 10 0 2 1 3 | 4 2 6 4 2 2 0 0 4 | 11 7 8 2 7 0 21 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0034.1.pfm: -------------------------------------------------------------------------------- 1 | 4 10 3 23 25 1 3 6 10 5 2 | 6 5 13 1 0 24 14 0 11 19 3 | 11 7 0 1 0 0 6 19 0 1 4 | 4 3 9 0 0 0 2 0 4 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0035.2.pfm: -------------------------------------------------------------------------------- 1 | 1423 708 2782 0 4000 27 3887 3550 799 1432 1487 2 | 560 1633 31 0 0 29 0 4 681 897 829 3 | 1242 1235 10 4000 0 109 6 383 2296 1360 1099 4 | 775 424 1177 0 0 3835 107 63 224 311 585 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0036.1.pfm: -------------------------------------------------------------------------------- 1 | 13 0 52 0 25 2 | 13 5 0 0 7 3 | 18 48 1 0 15 4 | 9 0 0 53 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0037.1.pfm: -------------------------------------------------------------------------------- 1 | 25 0 61 0 39 15 2 | 14 1 0 0 1 3 3 | 4 62 1 5 4 37 4 | 20 0 1 58 19 8 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0038.1.pfm: -------------------------------------------------------------------------------- 1 | 9 28 53 53 1 1 31 8 19 7 2 | 20 16 0 0 0 52 7 28 11 13 3 | 9 7 0 0 1 0 2 11 2 28 4 | 15 2 0 0 51 0 13 6 21 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0039.2.pfm: -------------------------------------------------------------------------------- 1 | 1468 88 14 14 277 22 42 264 123 254 2 | 81 9 13 36 1922 15 80 46 130 2858 3 | 1022 4237 4304 4281 11 4273 2179 3902 3789 280 4 | 1765 6 13 16 2139 34 2042 125 289 932 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0040.1.pfm: -------------------------------------------------------------------------------- 1 | 4 13 5 3 0 0 0 0 17 0 6 2 | 4 1 2 0 0 0 0 0 0 1 0 3 | 3 3 0 0 18 0 0 0 1 4 3 4 | 7 1 11 15 0 18 18 18 0 13 9 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0041.1.pfm: -------------------------------------------------------------------------------- 1 | 11 30 24 1 12 0 1 5 14 6 1 0 2 | 3 2 1 4 0 0 0 0 0 7 2 12 3 | 26 0 0 0 34 0 0 10 21 0 4 0 4 | 7 15 22 42 1 47 46 32 12 34 40 35 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0042.1.pfm: -------------------------------------------------------------------------------- 1 | 6 4 11 0 13 0 0 0 15 0 8 2 2 | 1 8 4 0 0 0 0 0 0 0 1 1 3 | 14 12 8 0 18 0 0 0 16 7 4 4 4 | 10 7 8 31 0 31 31 31 0 24 18 24 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0043.1.pfm: -------------------------------------------------------------------------------- 1 | 1 6 1 0 13 0 6 0 13 15 2 5 2 | 4 0 0 0 1 15 0 9 4 0 3 5 3 | 8 12 0 3 2 1 12 0 1 1 1 3 4 | 5 0 17 15 2 2 0 9 0 2 12 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0044.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 0 6 3 0 0 2 | 5 0 4 2 1 1 5 1 8 3 | 8 3 0 10 0 3 0 2 1 4 | 0 10 9 1 12 3 5 10 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA00445.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 0 20 0 0 2 0 1 4 6 2 | 8 25 17 0 0 0 0 0 2 10 1 3 | 7 0 0 0 0 3 27 0 4 6 1 4 | 13 4 12 9 29 26 0 29 22 9 21 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0045.1.pfm: -------------------------------------------------------------------------------- 1 | 3 7 9 3 11 11 11 3 4 3 8 8 9 9 11 2 2 | 5 0 1 6 0 0 0 3 1 4 5 1 0 5 0 7 3 | 4 3 1 4 3 2 2 2 8 6 1 4 2 0 3 0 4 | 2 4 3 1 0 1 1 6 1 1 0 1 3 0 0 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0046.1.pfm: -------------------------------------------------------------------------------- 1 | 5 1 1 1 20 16 1 8 14 2 0 13 8 5 2 | 0 0 0 0 0 2 0 2 0 0 4 1 8 13 3 | 14 20 0 0 0 1 0 4 1 0 0 3 3 0 4 | 2 0 20 20 1 2 20 7 6 19 17 4 2 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0047.2.pfm: -------------------------------------------------------------------------------- 1 | 1 221 1 1 1 736 2 338 50 417 131 129 2 | 1 3 1 3 1 4 725 77 265 6 53 195 3 | 1 582 1 36 175 67 2 3 58 24 482 290 4 | 805 3 806 769 634 3 81 391 436 360 140 189 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0048.1.pfm: -------------------------------------------------------------------------------- 1 | 13 13 3 1 54 1 1 1 0 3 2 5 2 | 13 39 5 53 0 1 50 1 0 37 0 17 3 | 17 2 37 0 0 52 3 0 53 8 37 12 4 | 11 0 9 0 0 0 0 52 1 6 15 20 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0049.1.pfm: -------------------------------------------------------------------------------- 1 | 1 6 9 4 13 16 16 14 15 9 2 | 5 8 3 3 1 0 0 0 1 2 3 | 8 2 4 1 0 0 0 2 0 2 4 | 2 0 0 8 2 0 0 0 0 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0050.1.pfm: -------------------------------------------------------------------------------- 1 | 6 19 19 20 5 0 1 20 19 20 1 1 2 | 4 0 0 0 3 10 1 0 1 0 13 13 3 | 10 1 0 0 11 0 18 0 0 0 6 1 4 | 0 0 1 0 1 10 0 0 0 0 0 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0051.1.pfm: -------------------------------------------------------------------------------- 1 | 0 2 12 11 12 2 0 0 12 12 12 0 0 5 6 6 5 3 2 | 4 0 0 0 0 0 6 0 0 0 0 6 7 2 0 1 2 6 3 | 7 10 0 0 0 10 0 12 0 0 0 6 2 3 2 1 1 1 4 | 1 0 0 1 0 0 6 0 0 0 0 0 3 2 4 4 4 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0052.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 57 2 9 6 37 2 56 6 2 | 50 0 1 1 0 0 0 0 0 0 3 | 0 0 0 0 0 0 0 0 2 50 4 | 7 58 0 55 49 52 21 56 0 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0053.1.pfm: -------------------------------------------------------------------------------- 1 | 15 15 15 0 3 2 | 0 0 0 0 9 3 | 0 0 0 15 0 4 | 0 0 0 0 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0054.1.pfm: -------------------------------------------------------------------------------- 1 | 19 64 63 4 10 10 13 3 28 2 | 3 1 0 62 27 2 8 17 1 3 | 2 2 2 3 16 53 0 1 0 4 | 46 3 5 1 17 5 49 49 41 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0055.1.pfm: -------------------------------------------------------------------------------- 1 | 7 9 4 0 16 7 0 6 0 0 6 0 2 | 8 0 2 15 0 0 15 0 0 10 0 0 3 | 1 7 10 1 0 9 1 0 16 6 0 16 4 | 0 0 0 0 0 0 0 10 0 0 10 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0056.1.pfm: -------------------------------------------------------------------------------- 1 | 3 0 2 0 0 18 2 | 5 0 0 0 0 0 3 | 4 19 18 19 20 2 4 | 8 1 0 1 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0057.1.pfm: -------------------------------------------------------------------------------- 1 | 1 2 15 0 0 0 0 3 10 8 2 | 4 0 1 0 0 2 0 1 0 2 3 | 7 7 0 11 15 14 14 8 4 4 4 | 4 7 0 5 1 0 2 4 2 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0058.1.pfm: -------------------------------------------------------------------------------- 1 | 6 11 5 0 16 0 1 0 0 6 2 | 1 1 7 17 1 17 0 0 0 3 3 | 6 5 1 0 0 0 16 0 17 5 4 | 4 0 4 0 0 0 0 17 0 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0059.1.pfm: -------------------------------------------------------------------------------- 1 | 7 15 2 1 21 0 1 0 0 1 3 2 | 1 1 9 20 0 20 0 1 0 1 5 3 | 9 4 9 0 0 0 20 0 21 18 0 4 | 4 1 1 0 0 1 0 20 0 1 13 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0060.1.pfm: -------------------------------------------------------------------------------- 1 | 34 16 7 58 51 0 2 112 116 0 14 66 13 39 36 25 2 | 37 33 51 14 4 116 113 0 0 1 65 6 20 43 9 35 3 | 27 26 25 41 56 0 1 1 0 0 33 42 73 22 47 29 4 | 18 41 33 3 5 0 0 3 0 115 4 2 10 12 24 27 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0061.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 1 25 19 7 1 2 2 0 2 | 0 0 0 0 13 1 2 17 35 36 3 | 38 38 37 13 1 3 2 0 0 0 4 | 0 0 0 0 5 27 33 19 1 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0062.2.pfm: -------------------------------------------------------------------------------- 1 | 32 70 0 0 991 989 94 56 154 264 233 2 | 768 914 0 0 1 2 32 261 137 262 357 3 | 188 4 990 991 1 0 866 37 603 415 224 4 | 1 1 1 0 0 2 0 637 96 49 176 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0063.1.pfm: -------------------------------------------------------------------------------- 1 | 7 0 17 17 0 4 2 2 | 0 4 0 0 0 2 1 3 | 1 0 0 0 7 0 11 4 | 9 13 0 0 10 11 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0064.1.pfm: -------------------------------------------------------------------------------- 1 | 16 16 16 0 1 2 | 0 0 0 0 9 3 | 0 0 0 16 1 4 | 0 0 0 0 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0065.2.pfm: -------------------------------------------------------------------------------- 1 | 94 101 390 100 139 145 71 819 522 713 82 41 22 54 676 2 | 317 166 23 3 15 129 547 21 48 5 2 9 99 555 58 3 | 320 127 368 671 674 395 179 15 270 137 767 693 263 144 47 4 | 126 464 79 87 34 193 66 8 23 9 12 120 479 109 81 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0066.1.pfm: -------------------------------------------------------------------------------- 1 | 3 3 19 0 1 0 2 26 5 5 4 1 2 22 1 0 3 22 5 7 2 | 8 0 0 1 0 1 23 1 15 7 2 0 5 5 27 25 12 5 12 0 3 | 14 0 9 27 26 4 3 0 4 10 18 2 20 0 0 0 0 0 6 1 4 | 3 25 0 0 1 23 0 1 4 6 4 25 1 1 0 3 13 1 5 20 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0067.1.pfm: -------------------------------------------------------------------------------- 1 | 10 7 3 0 26 2 2 1 2 | 7 1 2 28 1 17 0 11 3 | 5 21 0 1 3 1 19 11 4 | 9 2 26 2 1 11 10 8 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0068.1.pfm: -------------------------------------------------------------------------------- 1 | 7 20 16 11 13 11 6 9 5 5 6 7 8 6 10 4 3 7 4 9 5 5 7 6 3 7 3 1 6 3 2 | 2 0 2 1 1 3 1 1 3 11 11 7 7 5 5 8 6 8 9 6 7 6 11 9 12 9 12 11 11 13 3 | 11 1 1 1 3 1 2 1 6 1 4 5 2 1 4 4 4 3 3 2 5 2 0 1 2 2 2 3 1 2 4 | 1 0 2 8 4 6 12 10 7 4 0 2 4 9 2 5 8 3 5 4 4 8 3 5 4 3 4 6 3 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0069.1.pfm: -------------------------------------------------------------------------------- 1 | 2 2 4 39 3 1 1 21 1 2 36 11 1 1 2 | 4 2 26 2 34 0 37 2 4 14 0 11 5 0 3 | 4 0 1 1 1 41 4 2 1 25 6 13 3 17 4 | 33 39 12 1 5 1 1 18 37 2 1 8 34 25 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0070.1.pfm: -------------------------------------------------------------------------------- 1 | 5 3 16 1 0 17 17 0 0 16 12 8 2 | 6 9 1 1 18 1 0 0 18 1 0 2 3 | 2 3 1 0 0 0 0 1 0 0 1 2 4 | 5 3 0 16 0 0 1 17 0 1 5 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0071.1.pfm: -------------------------------------------------------------------------------- 1 | 15 9 6 11 21 0 0 0 0 25 2 | 1 1 12 2 0 0 0 0 25 0 3 | 2 0 4 5 4 25 25 0 0 0 4 | 7 15 3 7 0 0 0 25 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0072.1.pfm: -------------------------------------------------------------------------------- 1 | 9 17 15 35 23 2 0 28 0 0 0 0 36 15 2 | 8 2 0 1 0 12 0 0 0 0 0 36 0 6 3 | 8 7 3 0 0 13 0 8 36 36 0 0 0 10 4 | 11 10 18 0 13 9 36 0 0 0 36 0 0 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0073.1.pfm: -------------------------------------------------------------------------------- 1 | 3 1 3 0 7 9 8 4 0 11 4 1 3 4 2 4 4 4 1 4 2 | 8 10 8 11 4 2 3 6 11 0 7 10 8 6 9 5 5 6 7 4 3 | 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 3 2 4 | 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 1 1 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0074.1.pfm: -------------------------------------------------------------------------------- 1 | 3 0 0 0 0 9 4 2 2 5 0 0 1 0 7 2 | 0 0 0 0 9 0 2 4 0 0 0 0 0 9 1 3 | 7 10 9 0 0 1 0 2 8 5 10 0 0 0 2 4 | 0 0 1 10 1 0 4 2 0 0 0 10 9 1 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0075.1.pfm: -------------------------------------------------------------------------------- 1 | 52 59 0 0 58 2 | 2 0 0 0 0 3 | 4 0 1 0 1 4 | 1 0 58 59 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0076.1.pfm: -------------------------------------------------------------------------------- 1 | 16 0 0 0 0 20 16 4 1 2 | 1 20 20 0 0 0 0 1 6 3 | 2 0 0 20 20 0 0 15 0 4 | 1 0 0 0 0 0 4 0 13 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0077.1.pfm: -------------------------------------------------------------------------------- 1 | 24 54 59 0 65 71 4 24 9 2 | 7 6 4 72 4 2 0 6 9 3 | 31 7 0 2 0 1 1 38 55 4 | 14 9 13 2 7 2 71 8 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0078.1.pfm: -------------------------------------------------------------------------------- 1 | 7 8 3 30 0 0 0 0 0 2 | 9 8 18 0 1 0 0 0 17 3 | 6 4 1 0 0 0 31 2 10 4 | 9 11 9 1 30 31 0 29 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0079.2.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 4 2 0 1 0 6 3 2 | 32 30 35 27 5 28 31 24 25 26 3 | 1 1 0 0 15 1 0 3 0 3 4 | 2 4 0 4 13 6 3 8 4 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0080.2.pfm: -------------------------------------------------------------------------------- 1 | 33 4 4 42 41 5 3 2 | 3 0 0 0 0 3 5 3 | 6 37 38 0 1 33 2 4 | 0 1 0 0 0 1 32 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0081.1.pfm: -------------------------------------------------------------------------------- 1 | 31 4 24 2 1 48 47 2 | 0 14 16 0 0 0 0 3 | 0 29 7 47 47 0 0 4 | 18 2 2 0 1 1 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0082.1.pfm: -------------------------------------------------------------------------------- 1 | 11 0 24 16 23 17 24 8 14 1 14 25 21 7 2 | 14 22 0 2 0 0 1 0 1 1 5 5 2 5 3 | 1 0 4 1 0 0 0 1 15 28 1 0 3 8 4 | 4 8 2 11 7 13 5 21 0 0 10 0 4 10 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0083.1.pfm: -------------------------------------------------------------------------------- 1 | 2 9 0 1 32 3 46 1 43 15 2 2 2 | 1 33 45 45 1 1 0 0 0 1 0 1 3 | 39 2 1 0 0 0 0 0 0 0 44 43 4 | 4 2 0 0 13 42 0 45 3 30 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0084.1.pfm: -------------------------------------------------------------------------------- 1 | 5 8 15 18 25 0 28 27 7 2 | 5 3 0 3 0 26 0 0 0 3 | 10 4 3 3 0 0 0 1 2 4 | 8 13 10 4 3 2 0 0 19 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0085.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 0 0 0 3 0 10 10 5 1 1 4 3 4 2 2 | 3 4 0 0 0 0 0 0 0 5 7 2 2 1 3 1 3 | 3 0 10 0 10 7 10 0 0 0 1 4 2 4 2 2 4 | 3 6 0 10 0 0 0 0 0 0 1 3 2 2 1 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0086.1.pfm: -------------------------------------------------------------------------------- 1 | 0 39 3 2 0 0 2 | 39 0 0 0 0 0 3 | 1 0 37 38 0 38 4 | 0 1 0 0 40 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0087.1.pfm: -------------------------------------------------------------------------------- 1 | 8 21 22 0 23 22 0 2 | 4 0 0 22 0 1 0 3 | 3 1 1 0 0 0 0 4 | 8 1 0 1 0 0 23 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0088.1.pfm: -------------------------------------------------------------------------------- 1 | 0 6 2 0 2 1 0 0 9 0 4 6 0 0 0 4 3 2 1 3 2 | 3 2 3 3 1 7 10 10 1 1 4 2 0 1 10 5 1 3 1 6 3 | 4 1 1 2 0 0 0 0 0 4 2 2 1 6 0 0 1 0 7 1 4 | 3 1 4 5 7 2 0 0 0 5 0 0 9 3 0 1 5 5 1 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0089.1.pfm: -------------------------------------------------------------------------------- 1 | 7 29 0 1 34 0 2 | 11 2 0 0 0 26 3 | 10 3 0 32 0 2 4 | 6 0 34 1 0 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0090.1.pfm: -------------------------------------------------------------------------------- 1 | 1 9 0 12 0 0 0 0 5 1 2 0 2 | 6 0 12 0 0 0 12 11 0 7 4 2 3 | 1 3 0 0 0 0 0 0 0 4 3 8 4 | 4 0 0 0 12 12 0 1 7 0 3 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0091.1.pfm: -------------------------------------------------------------------------------- 1 | 13 9 39 20 0 44 0 12 0 0 0 4 2 | 14 10 0 24 43 0 1 32 0 0 3 4 3 | 8 20 3 0 1 0 11 0 0 43 20 2 4 | 9 5 2 0 0 0 32 0 44 1 21 34 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0092.1.pfm: -------------------------------------------------------------------------------- 1 | 4 10 2 0 0 0 0 9 16 5 2 | 8 0 2 28 0 0 3 14 0 4 3 | 10 15 1 0 0 29 25 1 3 4 4 | 7 4 24 1 29 0 1 5 10 16 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0093.1.pfm: -------------------------------------------------------------------------------- 1 | 0 30 0 1 0 0 9 2 | 30 0 28 0 1 0 2 3 | 0 0 0 29 1 30 14 4 | 0 0 2 0 28 0 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0094.2.pfm: -------------------------------------------------------------------------------- 1 | 3 0 0 17 20 0 0 14 2 | 5 0 0 0 0 0 0 0 3 | 3 0 0 0 0 0 6 6 4 | 9 20 20 3 0 20 14 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0095.1.pfm: -------------------------------------------------------------------------------- 1 | 6 0 0 17 0 3 2 | 1 16 17 0 0 8 3 | 7 0 0 0 0 3 4 | 3 1 0 0 17 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0096.1.pfm: -------------------------------------------------------------------------------- 1 | 15 0 0 35 0 0 0 2 | 15 0 0 0 35 0 0 3 | 5 0 35 0 0 35 0 4 | 0 35 0 0 0 0 35 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0097.1.pfm: -------------------------------------------------------------------------------- 1 | 1 17 0 0 33 0 0 0 0 1 11 1 2 | 0 0 0 0 0 33 0 0 1 0 20 32 3 | 31 16 0 33 0 0 33 0 32 22 1 0 4 | 1 0 33 0 0 0 0 33 0 10 1 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0098.1.pfm: -------------------------------------------------------------------------------- 1 | 4 17 0 0 0 5 2 | 16 0 1 39 39 3 3 | 4 0 0 1 0 17 4 | 16 23 39 0 1 15 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0099.2.pfm: -------------------------------------------------------------------------------- 1 | 0 0 16 5 3 0 16 2 | 1 0 2 12 0 15 0 3 | 0 15 0 1 1 3 1 4 | 17 3 0 0 14 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0100.1.pfm: -------------------------------------------------------------------------------- 1 | 8 22 2 16 1 2 0 6 2 | 4 1 48 17 0 1 0 0 3 | 34 25 1 16 50 0 0 44 4 | 5 3 0 2 0 48 51 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0101.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 1 5 6 5 1 2 0 1 2 | 5 1 0 1 5 1 0 0 15 16 3 | 8 15 15 9 3 1 0 0 0 0 4 | 4 1 1 2 3 10 16 15 2 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0102.2.pfm: -------------------------------------------------------------------------------- 1 | 3 1 4 2 4 2 18 18 0 2 | 0 1 1 9 2 15 0 0 6 3 | 0 4 6 2 10 0 0 0 2 4 | 15 12 7 5 2 1 0 0 10 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0103.1.pfm: -------------------------------------------------------------------------------- 1 | 1 38 0 0 0 10 2 | 34 0 40 38 1 1 3 | 1 2 1 3 0 16 4 | 5 1 0 0 40 14 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0104.2.pfm: -------------------------------------------------------------------------------- 1 | 153 39 7 414 0 31 24 0 27 61 2 | 159 170 431 0 421 1 97 0 49 265 3 | 63 196 0 18 8 405 2 411 324 40 4 | 63 33 0 6 9 1 315 27 38 72 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0105.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 2 11 5 0 0 0 0 1 2 | 0 0 0 0 1 0 5 13 17 18 15 3 | 18 18 18 16 6 2 2 0 0 0 1 4 | 0 0 0 0 0 11 11 5 1 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0106.1.pfm: -------------------------------------------------------------------------------- 1 | 5 3 4 5 13 0 17 0 0 0 0 0 1 1 4 1 15 2 1 1 2 | 8 7 0 0 0 17 0 0 0 11 16 16 0 0 0 14 0 0 1 2 3 | 2 6 13 12 4 0 0 0 17 0 0 0 15 14 13 2 0 0 14 1 4 | 2 1 0 0 0 0 0 17 0 6 1 1 1 2 0 0 2 15 1 13 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0107.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 11 10 2 0 0 0 0 2 | 4 0 0 0 3 0 0 2 18 18 3 | 11 17 18 7 4 0 0 0 0 0 4 | 3 1 0 0 1 16 18 16 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0108.2.pfm: -------------------------------------------------------------------------------- 1 | 61 16 352 3 354 268 360 222 155 56 83 82 82 68 77 2 | 145 46 0 10 0 0 3 2 44 135 147 127 118 107 101 3 | 152 18 2 2 5 0 20 44 157 150 128 128 128 139 140 4 | 31 309 35 374 30 121 6 121 33 48 31 52 61 75 71 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0109.1.pfm: -------------------------------------------------------------------------------- 1 | 16 20 26 0 25 0 24 0 15 12 2 | 10 12 33 59 0 0 5 0 14 12 3 | 12 5 0 0 0 0 12 22 14 10 4 | 13 16 0 0 34 59 18 37 8 15 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0110.1.pfm: -------------------------------------------------------------------------------- 1 | 3 1 30 37 0 2 37 0 0 2 | 19 29 6 0 0 5 0 0 0 3 | 9 4 0 0 0 10 0 0 0 4 | 6 3 1 0 37 20 0 37 37 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0111.1.pfm: -------------------------------------------------------------------------------- 1 | 9 0 2 0 1 8 6 1 10 0 2 2 | 0 2 0 0 0 0 0 9 0 1 8 3 | 3 9 10 11 1 0 2 2 2 9 2 4 | 0 1 0 1 10 4 4 0 0 2 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0112.2.pfm: -------------------------------------------------------------------------------- 1 | 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 26 2 | 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 165 3 | 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 22 4 | 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61 262 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0113.1.pfm: -------------------------------------------------------------------------------- 1 | 3 4 3 7 6 1 8 2 3 5 1 0 1 2 0 1 4 3 2 | 2 0 0 0 1 6 0 0 2 3 3 0 0 4 8 2 0 1 3 | 4 5 6 1 1 2 1 2 0 0 0 8 0 0 1 1 4 2 4 | 0 0 0 1 1 0 0 5 4 1 5 1 8 3 0 5 1 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0114.1.pfm: -------------------------------------------------------------------------------- 1 | 28 2 12 5 3 59 53 56 4 6 3 4 42 2 | 7 2 4 23 51 1 2 1 4 2 22 49 7 3 | 27 56 35 20 4 3 10 8 58 33 11 5 10 4 | 5 7 16 19 9 4 2 2 1 26 31 9 8 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0115.1.pfm: -------------------------------------------------------------------------------- 1 | 17 17 20 0 0 0 0 25 24 25 0 0 0 0 25 20 0 2 | 5 1 0 0 0 0 25 0 0 0 0 0 0 25 0 1 15 3 | 0 5 5 25 24 0 0 0 0 0 25 25 0 0 0 2 6 4 | 3 2 0 0 1 25 0 0 1 0 0 0 25 0 0 2 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0116.1.pfm: -------------------------------------------------------------------------------- 1 | 7 0 16 17 0 0 1 24 13 0 0 0 0 0 11 2 | 4 16 17 16 33 33 17 0 0 0 0 0 0 8 22 3 | 22 17 0 0 0 0 0 0 16 33 33 17 16 16 0 4 | 0 0 0 0 0 0 15 9 4 0 0 16 17 9 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0117.1.pfm: -------------------------------------------------------------------------------- 1 | 0 1 0 1 12 3 3 2 2 | 0 12 3 0 2 8 1 5 3 | 15 1 1 12 0 1 7 5 4 | 0 1 11 2 1 3 4 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0118.1.pfm: -------------------------------------------------------------------------------- 1 | 5 9 0 0 3 0 5 5 13 2 | 15 2 0 0 4 0 7 14 14 3 | 6 23 42 42 23 42 15 4 10 4 | 16 8 0 0 12 0 15 19 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0119.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 14 2 2 7 4 0 0 0 16 14 2 | 0 0 0 16 1 8 8 1 3 0 16 16 0 0 3 | 0 16 16 0 0 5 4 5 2 16 0 0 0 1 4 | 16 0 0 0 1 1 2 3 7 0 0 0 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0120.1.pfm: -------------------------------------------------------------------------------- 1 | 1 3 1 0 0 2 3 1 8 0 0 2 2 | 1 3 2 9 13 11 8 1 5 6 17 0 3 | 2 4 9 3 4 4 2 1 1 7 0 18 4 | 20 14 12 12 7 7 11 21 10 11 7 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0121.1.pfm: -------------------------------------------------------------------------------- 1 | 14 0 14 0 4 1 0 3 2 | 1 0 0 0 6 8 0 6 3 | 0 15 1 0 0 0 9 4 4 | 0 0 0 15 5 6 6 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0122.1.pfm: -------------------------------------------------------------------------------- 1 | 4 1 13 24 0 0 6 4 9 2 | 7 4 1 0 0 0 0 6 7 3 | 4 5 7 0 24 0 18 12 5 4 | 9 14 3 0 0 24 0 2 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0123.1.pfm: -------------------------------------------------------------------------------- 1 | 0 12 0 0 1 0 5 3 3 4 2 | 49 0 20 23 3 45 28 25 31 26 3 | 0 37 29 1 45 4 6 11 5 7 4 | 0 0 0 25 0 0 10 10 10 12 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0124.1.pfm: -------------------------------------------------------------------------------- 1 | 13 0 20 0 1 1 19 2 | 1 1 0 19 0 0 0 3 | 3 0 0 0 0 0 1 4 | 3 19 0 1 19 19 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0125.1.pfm: -------------------------------------------------------------------------------- 1 | 0 36 38 1 2 15 4 2 2 | 1 0 0 1 0 0 12 13 3 | 0 0 0 2 4 22 18 6 4 | 37 2 0 34 32 1 4 17 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0126.1.pfm: -------------------------------------------------------------------------------- 1 | 10 1 4 20 21 0 7 0 5 2 | 4 4 2 0 0 21 5 0 4 3 | 0 14 2 0 0 0 3 21 2 4 | 7 2 13 1 0 0 6 0 10 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0127.1.pfm: -------------------------------------------------------------------------------- 1 | 30 6 1 4 3 0 2 32 4 2 2 | 2 19 0 0 33 2 0 7 3 5 3 | 8 7 2 4 2 2 1 2 0 14 4 | 2 10 39 34 4 38 39 1 35 21 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0128.1.pfm: -------------------------------------------------------------------------------- 1 | 9 1 13 0 0 0 0 0 2 | 0 7 0 12 0 0 1 1 3 | 0 4 0 0 13 0 12 12 4 | 4 1 0 1 0 13 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0129.1.pfm: -------------------------------------------------------------------------------- 1 | 4 13 0 2 1 0 13 2 | 4 0 14 0 0 15 0 3 | 0 1 0 13 0 0 1 4 | 7 1 1 0 14 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0130.1.pfm: -------------------------------------------------------------------------------- 1 | 7 3 0 0 16 0 2 | 6 2 16 16 0 15 3 | 3 0 0 0 0 1 4 | 0 11 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0131.1.pfm: -------------------------------------------------------------------------------- 1 | 2 13 20 2 0 0 0 0 0 2 2 | 6 1 0 17 0 1 19 18 0 13 3 | 5 0 0 1 19 0 0 2 19 1 4 | 7 6 0 0 1 19 1 0 1 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0132.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 31 31 0 1 2 | 19 0 0 0 0 1 3 | 5 0 0 0 1 10 4 | 6 31 0 0 30 19 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0133.1.pfm: -------------------------------------------------------------------------------- 1 | 15 4 41 36 7 19 3 2 | 11 35 1 2 29 14 22 3 | 10 2 1 4 6 7 15 4 | 7 2 0 1 1 3 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0135.1.pfm: -------------------------------------------------------------------------------- 1 | 9 16 19 0 0 19 20 2 0 16 9 2 2 2 | 0 2 0 0 0 0 0 2 1 1 0 8 9 3 | 3 2 0 0 0 0 0 0 0 0 3 0 3 4 | 8 0 1 20 20 1 0 16 19 3 8 10 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0136.1.pfm: -------------------------------------------------------------------------------- 1 | 12 29 2 14 0 0 0 4 4 2 | 9 3 20 0 1 44 44 3 8 3 | 3 7 5 1 0 0 0 11 11 4 | 20 5 17 29 43 0 0 26 21 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0137.2.pfm: -------------------------------------------------------------------------------- 1 | 208 859 251 10 8 106 23 528 696 53 1900 2030 954 336 417 2 | 1076 496 574 22 14 1921 1900 762 31 30 124 17 263 760 804 3 | 415 279 144 11 38 14 7 115 1292 1700 29 23 552 270 425 4 | 378 446 1112 2038 2023 44 155 680 66 302 32 15 315 714 431 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0138.2.pfm: -------------------------------------------------------------------------------- 1 | 211 58 76 1452 34 122 1575 3 35 913 219 39 20 1406 13 1574 42 205 366 213 179 2 | 174 269 1366 30 44 978 7 1586 1481 201 375 7 5 112 1280 9 13 1007 31 933 1114 3 | 366 146 50 94 1516 323 12 12 20 162 124 1551 1577 34 233 7 1530 183 688 319 37 4 | 840 1124 105 26 10 182 12 5 70 329 886 7 2 51 74 10 9 198 507 125 260 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0139.1.pfm: -------------------------------------------------------------------------------- 1 | 87 167 281 56 8 744 40 107 851 5 333 54 12 56 104 372 82 117 402 2 | 291 145 49 800 903 13 528 433 11 0 3 12 0 8 733 13 482 322 181 3 | 76 414 449 21 0 65 334 48 32 903 566 504 890 775 5 507 307 73 266 4 | 459 187 134 36 2 91 11 324 18 3 9 341 8 71 67 17 37 396 59 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0140.1.pfm: -------------------------------------------------------------------------------- 1 | 400 261 131 265 669 701 664 713 734 996 527 1959 3 2928 16 2770 2382 547 2 | 1329 444 182 746 635 687 745 699 662 407 1172 31 7 7 26 6 51 550 3 | 618 520 1921 1228 775 903 938 891 862 940 901 37 2936 2 30 23 376 1601 4 | 595 1717 710 706 866 654 599 644 691 603 345 920 0 10 2873 144 134 242 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0141.1.pfm: -------------------------------------------------------------------------------- 1 | 1054 673 420 259 310 3326 3567 32 21 182 9 3458 2 | 800 829 1211 1250 2664 32 2 5 12 46 3376 20 3 | 985 1370 1209 448 627 248 60 3586 3602 244 170 129 4 | 793 767 805 1693 52 50 27 31 17 3175 85 27 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0142.1.pfm: -------------------------------------------------------------------------------- 1 | 63 579 11 47 118 415 206 1235 17 10 14 1050 887 1200 198 2 | 846 58 50 12 363 18 365 30 5 16 1029 16 68 33 119 3 | 66 28 36 79 825 29 186 24 15 1239 129 30 315 75 207 4 | 389 701 1270 1231 63 907 612 80 1332 104 196 269 92 53 837 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0143.1.pfm: -------------------------------------------------------------------------------- 1 | 27 20 327 2 14 38 85 64 408 26 27 32 426 366 485 2 | 444 453 7 10 1 83 4 194 124 39 77 422 41 67 60 3 | 89 22 4 7 6 529 9 77 38 26 444 84 36 157 61 4 | 107 174 331 650 648 19 570 333 96 575 117 127 161 74 58 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0144.1.pfm: -------------------------------------------------------------------------------- 1 | 20 13 38 6 321 8 6 585 606 191 2 | 19 10 552 541 21 0 2 21 1 15 3 | 25 129 9 1 148 605 592 7 5 393 4 | 549 461 14 65 123 0 13 0 1 14 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0145.1.pfm: -------------------------------------------------------------------------------- 1 | 8 285 2425 24 717 402 711 1461 2583 1612 15 252 2187 49 2 | 3763 3289 21 97 1374 1182 1624 920 285 210 3815 3316 30 118 3 | 255 22 1125 3945 105 254 618 1032 781 1269 224 12 1247 3886 4 | 40 477 508 13 1890 2248 1135 677 441 996 34 503 612 17 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0146.1.pfm: -------------------------------------------------------------------------------- 1 | 50 60 91 72 10 6 30 191 9 0 1 0 0 84 2 | 177 170 151 49 297 362 125 154 2 3 480 480 2 122 3 | 179 172 199 298 144 2 182 121 469 477 0 0 0 219 4 | 70 75 37 60 30 111 144 15 1 1 0 1 479 56 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0147.1.pfm: -------------------------------------------------------------------------------- 1 | 67 34 8 217 0 19 9 0 0 45 2 | 96 53 219 4 212 2 44 2 17 107 3 | 36 130 0 5 3 204 0 216 183 24 4 | 28 10 0 1 12 2 174 9 27 51 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0148.1.pfm: -------------------------------------------------------------------------------- 1 | 13 108 1 5 6 476 6 291 45 378 90 2 | 2 7 7 7 3 12 807 106 368 9 125 3 | 2 770 5 24 78 368 5 5 69 24 466 4 | 875 8 882 860 809 40 79 495 414 482 211 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0149.1.pfm: -------------------------------------------------------------------------------- 1 | 0 2 104 104 1 2 103 102 0 0 99 105 0 0 100 102 5 3 2 | 0 0 0 0 0 0 0 0 0 2 4 0 0 2 3 0 0 3 3 | 105 103 1 1 104 102 2 3 104 103 2 0 105 103 0 2 97 97 4 | 0 0 0 0 0 1 0 0 1 0 0 0 0 0 2 1 3 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0150.1.pfm: -------------------------------------------------------------------------------- 1 | 10 0 0 20 0 6 5 16 0 0 15 2 | 1 0 0 0 17 2 10 0 0 20 2 3 | 9 0 19 0 1 1 1 2 20 0 2 4 | 0 20 1 0 2 11 4 2 0 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0151.1.pfm: -------------------------------------------------------------------------------- 1 | 27 0 1 27 27 20 2 | 0 0 9 0 0 0 3 | 0 0 0 0 0 1 4 | 0 27 17 0 0 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0152.1.pfm: -------------------------------------------------------------------------------- 1 | 3 1 1 0 1 0 18 2 | 1 2 1 0 25 26 3 3 | 2 2 0 0 0 0 1 4 | 20 21 24 26 0 0 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0153.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 8 7 0 5 3 0 0 8 9 0 2 | 3 3 1 1 0 0 0 0 0 0 0 8 3 | 0 0 0 1 0 4 1 1 0 1 0 0 4 | 6 6 0 0 9 0 5 8 9 0 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0154.1.pfm: -------------------------------------------------------------------------------- 1 | 11 0 1 2 11 16 0 2 0 21 2 | 9 22 16 20 9 1 0 0 0 0 3 | 2 0 1 0 0 5 25 23 25 4 4 | 3 3 7 3 5 3 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0155.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 0 6 16 0 0 0 0 0 3 10 2 | 0 0 8 15 0 0 1 0 0 2 16 0 3 | 4 20 3 0 0 24 23 24 24 16 0 12 4 | 19 4 13 3 8 0 0 0 0 6 5 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0156.1.pfm: -------------------------------------------------------------------------------- 1 | 2 9 0 0 13 12 7 0 2 | 9 3 0 0 0 0 0 0 3 | 1 1 13 13 0 0 6 0 4 | 1 0 0 0 0 1 0 13 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0157.1.pfm: -------------------------------------------------------------------------------- 1 | 0 1 3 13 12 13 0 12 2 | 0 2 0 0 1 0 12 0 3 | 5 10 1 0 0 0 0 0 4 | 8 0 9 0 0 0 1 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0158.1.pfm: -------------------------------------------------------------------------------- 1 | 2 7 0 6 14 14 0 0 2 | 13 0 7 0 0 0 0 1 3 | 0 5 5 1 0 2 0 6 4 | 0 4 4 9 2 0 16 9 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0159.1.pfm: -------------------------------------------------------------------------------- 1 | 12 0 1 0 0 22 4 5 5 13 5 17 1 0 2 1 21 2 | 0 0 0 0 18 0 7 8 4 1 6 3 1 1 1 17 0 3 | 11 23 13 1 3 1 5 9 11 7 12 3 20 16 3 3 1 4 | 0 0 9 22 2 0 7 1 3 2 0 0 1 6 17 2 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0160.1.pfm: -------------------------------------------------------------------------------- 1 | 8 13 0 3 2 0 14 3 2 | 1 0 0 0 2 13 0 8 3 | 3 1 13 11 0 0 0 2 4 | 1 0 1 0 10 1 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0161.1.pfm: -------------------------------------------------------------------------------- 1 | 358 81 81 91 1226 3298 2 | 1832 67 67 88 5364 981 3 | 176 300 6713 6643 160 1186 4 | 4546 6464 51 90 162 1447 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0162.1.pfm: -------------------------------------------------------------------------------- 1 | 3 2 0 0 0 3 1 0 2 0 1 2 | 4 1 13 0 0 0 0 0 10 0 0 3 | 1 12 0 15 3 12 14 15 0 15 7 4 | 7 0 2 0 12 0 0 0 3 0 7 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0163.1.pfm: -------------------------------------------------------------------------------- 1 | 0 3 0 0 0 0 4 12 11 2 0 0 0 2 2 | 0 0 0 0 14 15 10 0 5 0 0 0 0 0 3 | 18 14 18 17 4 1 1 0 2 14 18 18 16 16 4 | 0 1 0 1 0 2 3 6 0 2 0 0 2 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0164.1.pfm: -------------------------------------------------------------------------------- 1 | 4 23 23 0 0 0 0 2 | 12 0 0 1 23 0 0 3 | 2 0 0 22 0 0 0 4 | 5 0 0 0 0 23 23 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0165.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 5 21 0 3 13 2 | 0 0 0 0 3 0 0 3 | 0 0 0 0 0 11 5 4 | 20 21 16 0 18 7 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0166.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 16 16 0 0 15 2 | 1 0 0 0 0 0 0 3 | 0 0 0 0 0 9 1 4 | 14 16 0 0 16 7 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0167.1.pfm: -------------------------------------------------------------------------------- 1 | 3 1 33 40 0 0 34 2 | 16 0 0 0 0 0 0 3 | 0 0 7 0 1 8 4 4 | 21 39 0 0 39 32 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0168.1.pfm: -------------------------------------------------------------------------------- 1 | 4 0 21 21 8 1 1 2 | 4 0 0 0 0 7 0 3 | 0 0 0 0 0 0 20 4 | 13 21 0 0 13 13 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0169.1.pfm: -------------------------------------------------------------------------------- 1 | 6 0 21 21 5 3 0 2 | 2 0 0 0 0 1 0 3 | 1 0 0 0 0 2 21 4 | 12 21 0 0 16 15 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0170.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 17 19 6 0 10 2 | 1 0 0 0 2 3 0 3 | 0 0 0 0 0 6 9 4 | 17 19 2 0 11 10 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0171.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 13 13 1 2 1 2 | 3 0 0 0 0 1 0 3 | 0 0 0 0 0 2 12 4 | 10 13 0 0 12 8 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0172.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 15 15 0 0 15 2 | 3 2 0 0 0 0 0 3 | 0 0 0 0 0 0 0 4 | 12 13 0 0 15 15 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0173.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 10 17 0 17 0 2 | 0 0 0 0 17 0 0 3 | 0 0 3 0 0 0 0 4 | 16 17 4 0 0 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0174.1.pfm: -------------------------------------------------------------------------------- 1 | 2 2 6 16 0 0 13 2 | 0 0 0 0 0 2 0 3 | 0 0 2 0 0 6 3 4 | 14 14 8 0 16 8 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0175.1.pfm: -------------------------------------------------------------------------------- 1 | 2 0 21 21 0 3 8 2 | 7 0 0 0 0 0 0 3 | 1 0 0 0 0 4 13 4 | 11 21 0 0 21 14 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0176.1.pfm: -------------------------------------------------------------------------------- 1 | 2 2 21 32 0 0 16 2 | 3 3 0 0 0 0 0 3 | 3 0 6 0 0 2 16 4 | 24 27 5 0 32 30 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0177.1.pfm: -------------------------------------------------------------------------------- 1 | 4 0 25 25 0 0 23 2 | 10 0 0 0 0 1 0 3 | 1 0 0 0 0 8 2 4 | 10 25 0 0 25 16 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0178.1.pfm: -------------------------------------------------------------------------------- 1 | 2 2 17 19 0 0 15 2 | 4 0 0 0 0 0 0 3 | 0 0 0 0 1 1 4 4 | 13 17 2 0 18 18 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0179.1.pfm: -------------------------------------------------------------------------------- 1 | 2 0 23 23 0 0 12 2 | 6 0 0 0 0 0 0 3 | 2 0 0 0 0 2 10 4 | 13 23 0 0 23 21 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0180.1.pfm: -------------------------------------------------------------------------------- 1 | 1 2 0 13 13 0 0 10 1 2 | 1 2 0 0 0 0 0 0 2 3 | 5 0 0 0 0 0 0 3 10 4 | 6 9 13 0 0 13 13 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0181.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 22 22 0 2 15 2 | 8 0 0 0 0 0 0 3 | 1 0 0 0 0 3 6 4 | 12 22 0 0 22 17 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0182.1.pfm: -------------------------------------------------------------------------------- 1 | 12 7 13 30 0 0 15 2 | 2 1 0 0 0 0 0 3 | 3 0 0 0 0 6 15 4 | 13 22 17 0 30 24 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0183.1.pfm: -------------------------------------------------------------------------------- 1 | 7 0 0 21 26 0 7 22 2 | 3 7 6 0 0 3 0 0 3 | 2 0 7 2 0 3 1 4 4 | 14 19 13 3 0 20 18 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0184.1.pfm: -------------------------------------------------------------------------------- 1 | 2 0 18 20 0 0 14 2 | 9 0 0 0 0 0 0 3 | 3 0 0 0 0 1 6 4 | 6 20 2 0 20 19 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0185.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 0 1 2 | 3 0 10 0 0 3 3 | 0 0 0 10 5 4 4 | 7 10 0 0 5 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0186.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 24 24 0 1 21 2 | 4 0 0 0 0 0 0 3 | 3 0 0 0 0 19 3 4 | 16 24 0 0 24 4 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0187.1.pfm: -------------------------------------------------------------------------------- 1 | 1 22 23 0 3 10 1 2 | 0 0 0 0 0 0 12 3 | 0 1 0 0 3 9 4 4 | 22 0 0 23 17 4 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0188.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 21 21 0 0 21 2 | 13 16 0 0 0 0 0 3 | 6 0 0 0 0 0 0 4 | 1 5 0 0 21 21 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0189.1.pfm: -------------------------------------------------------------------------------- 1 | 5 3 43 42 1 5 34 2 | 15 0 0 0 0 0 0 3 | 6 0 0 0 1 16 9 4 | 17 40 0 1 41 22 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0190.1.pfm: -------------------------------------------------------------------------------- 1 | 0 22 22 0 0 0 2 | 0 0 0 0 22 14 3 | 0 0 0 0 0 2 4 | 22 0 0 22 0 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0191.1.pfm: -------------------------------------------------------------------------------- 1 | 4 0 20 20 0 1 15 2 | 2 0 0 0 0 0 0 3 | 3 0 0 0 0 6 5 4 | 11 20 0 0 20 13 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0192.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 20 20 1 0 4 2 | 3 0 0 0 0 3 0 3 | 0 0 0 0 0 0 16 4 | 16 20 0 0 19 17 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0193.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 17 1 0 18 12 2 | 19 9 2 18 12 0 0 3 | 0 0 0 0 0 1 4 4 | 0 10 0 0 7 0 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0194.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 18 18 0 0 17 2 | 2 0 0 0 0 0 0 3 | 0 0 0 0 0 0 1 4 | 16 18 0 0 18 18 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0195.1.pfm: -------------------------------------------------------------------------------- 1 | 3 4 16 20 0 0 16 2 | 7 0 0 0 0 2 0 3 | 2 0 3 0 0 4 4 4 | 8 16 1 0 20 14 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0196.1.pfm: -------------------------------------------------------------------------------- 1 | 5 0 33 35 4 6 13 2 | 5 0 0 0 0 0 0 3 | 1 0 2 0 5 7 22 4 | 24 35 0 0 26 22 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0197.1.pfm: -------------------------------------------------------------------------------- 1 | 2 8 1 22 22 0 2 15 2 | 4 3 0 0 0 0 3 1 3 | 7 0 0 0 0 0 6 1 4 | 9 11 21 0 0 22 11 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0198.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 22 22 0 0 13 2 | 11 0 0 0 0 0 0 3 | 4 0 0 0 0 0 8 4 | 7 22 0 0 22 22 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0199.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 27 0 26 2 | 5 0 0 0 0 3 | 0 27 0 0 1 4 | 22 0 0 27 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0200.1.pfm: -------------------------------------------------------------------------------- 1 | 6 0 21 21 0 0 13 2 | 8 0 0 0 0 1 1 3 | 3 0 0 0 0 0 6 4 | 4 21 0 0 21 20 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0201.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 20 20 0 0 0 2 | 5 0 0 0 0 20 19 3 | 1 0 0 0 0 0 0 4 | 14 20 0 0 20 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0202.1.pfm: -------------------------------------------------------------------------------- 1 | 3 0 27 27 0 0 17 2 | 13 0 0 0 0 0 0 3 | 0 0 0 0 0 0 10 4 | 11 27 0 0 27 27 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0203.1.pfm: -------------------------------------------------------------------------------- 1 | 3 0 25 25 0 0 23 2 | 7 0 0 0 0 0 0 3 | 0 0 0 0 0 18 2 4 | 15 25 0 0 25 7 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0204.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 20 0 20 1 2 | 0 0 0 7 0 19 3 | 0 20 0 4 0 0 4 | 20 0 0 9 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0205.1.pfm: -------------------------------------------------------------------------------- 1 | 4 6 12 0 3 1 13 5 7 9 2 | 22 23 6 64 0 70 0 54 13 33 3 | 9 11 30 3 14 0 2 7 11 10 4 | 36 31 23 4 54 0 56 5 40 19 5 | -------------------------------------------------------------------------------- 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19 19 0 0 16 2 | 10 0 0 0 0 0 0 3 | 0 0 0 0 0 6 3 4 | 7 18 0 0 19 13 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0210.1.pfm: -------------------------------------------------------------------------------- 1 | 14 23 34 0 34 2 | 0 0 0 34 0 3 | 5 0 0 0 0 4 | 15 11 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0211.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 23 23 0 1 7 2 | 0 0 0 0 0 0 0 3 | 1 0 0 0 23 0 16 4 | 22 23 0 0 0 22 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0212.1.pfm: -------------------------------------------------------------------------------- 1 | 0 20 22 0 0 0 2 | 0 0 0 0 22 21 3 | 0 0 0 1 0 0 4 | 22 2 0 21 0 1 5 | 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/parse_motifs/jaspar/jaspar_raw/MA0216.1.pfm: -------------------------------------------------------------------------------- 1 | 3 1 8 37 3 3 18 2 | 2 0 0 0 0 0 0 3 | 3 0 2 1 0 9 19 4 | 30 37 28 0 35 26 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0217.1.pfm: -------------------------------------------------------------------------------- 1 | 4 14 19 0 19 2 | 1 0 0 19 0 3 | 2 2 0 0 0 4 | 12 3 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0218.1.pfm: -------------------------------------------------------------------------------- 1 | 0 1 9 20 17 0 2 | 6 2 0 0 0 19 3 | 0 0 11 0 1 1 4 | 14 17 0 0 2 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0219.1.pfm: -------------------------------------------------------------------------------- 1 | 3 3 19 19 0 0 14 2 | 7 0 0 0 0 1 0 3 | 1 0 0 1 0 10 6 4 | 9 17 1 0 20 9 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0220.1.pfm: -------------------------------------------------------------------------------- 1 | 2 0 23 23 0 0 13 2 | 8 0 0 0 0 0 0 3 | 2 0 0 0 0 2 10 4 | 11 23 0 0 23 21 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0221.1.pfm: -------------------------------------------------------------------------------- 1 | 3 1 22 22 0 0 17 2 | 10 0 0 0 2 2 0 3 | 0 0 0 0 1 11 4 4 | 9 21 0 0 19 9 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0222.1.pfm: -------------------------------------------------------------------------------- 1 | 4 1 0 0 0 17 0 11 2 | 4 0 0 0 0 0 12 0 3 | 4 2 0 0 17 0 0 6 4 | 5 14 17 17 0 0 5 0 5 | 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-------------------------------------------------------------------------------- 1 | 2 0 17 17 0 0 9 2 | 2 0 0 0 0 0 0 3 | 2 0 0 0 0 0 7 4 | 11 17 0 0 17 17 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0227.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 17 0 14 0 2 | 0 0 0 17 0 0 3 | 0 17 0 0 3 8 4 | 17 0 0 0 0 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0228.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 21 21 0 0 19 2 | 12 0 0 0 0 0 0 3 | 0 0 0 0 1 8 2 4 | 9 21 0 0 20 13 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0229.1.pfm: -------------------------------------------------------------------------------- 1 | 4 1 0 16 16 0 0 11 2 | 0 9 0 0 0 0 0 0 3 | 3 0 0 0 0 0 0 5 4 | 9 6 16 0 0 16 16 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0230.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 16 16 1 0 16 2 | 3 0 0 0 0 0 0 3 | 0 0 0 0 0 6 0 4 | 12 16 0 0 15 10 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0231.1.pfm: -------------------------------------------------------------------------------- 1 | 0 22 22 1 4 19 2 | 0 0 0 10 5 0 3 | 0 0 0 2 3 3 4 | 22 0 0 9 10 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0232.1.pfm: -------------------------------------------------------------------------------- 1 | 0 23 23 0 1 17 2 | 0 0 0 5 3 0 3 | 0 0 0 0 7 6 4 | 23 0 0 18 12 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0233.1.pfm: -------------------------------------------------------------------------------- 1 | 20 29 41 0 41 2 | 1 0 0 41 0 3 | 1 2 0 0 0 4 | 19 10 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0234.1.pfm: -------------------------------------------------------------------------------- 1 | 0 19 19 0 0 0 2 | 0 0 0 0 19 17 3 | 0 0 0 2 0 1 4 | 19 0 0 17 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0235.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 0 15 0 0 5 2 | 2 0 0 0 0 0 0 3 | 0 0 15 0 0 0 4 4 | 12 15 0 0 15 15 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0236.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 20 20 0 0 15 2 | 6 1 0 0 0 1 0 3 | 2 0 0 0 0 4 3 4 | 11 19 0 0 20 15 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0237.1.pfm: -------------------------------------------------------------------------------- 1 | 4 2 2 2 0 17 8 7 2 | 10 3 0 0 2 0 0 11 3 | 3 0 1 0 20 5 0 3 4 | 8 20 22 23 3 3 17 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0238.1.pfm: -------------------------------------------------------------------------------- 1 | 4 0 24 24 0 0 24 2 | 9 0 0 0 0 0 0 3 | 0 0 0 0 0 11 0 4 | 11 24 0 0 24 13 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0239.1.pfm: -------------------------------------------------------------------------------- 1 | 10 1 4 20 21 0 7 0 5 2 | 4 4 2 0 0 21 5 0 4 3 | 0 14 2 0 0 0 3 21 2 4 | 7 2 13 1 0 0 6 0 10 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0240.1.pfm: -------------------------------------------------------------------------------- 1 | 1 1 27 28 0 0 21 2 | 4 0 0 0 0 0 0 3 | 4 0 0 0 0 0 7 4 | 19 27 1 0 28 28 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0241.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 23 23 0 0 19 2 | 12 0 0 0 0 0 0 3 | 3 0 0 0 0 3 4 4 | 7 23 0 0 23 20 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0242.1.pfm: -------------------------------------------------------------------------------- 1 | 12 27 28 0 0 5 0 28 20 2 | 2 0 0 29 28 1 29 0 0 3 | 0 1 1 0 1 23 0 0 9 4 | 15 1 0 0 0 0 0 1 0 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | 0 0 27 0 27 0 2 | 0 0 0 0 0 10 3 | 1 27 0 1 0 0 4 | 26 0 0 26 0 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0247.1.pfm: -------------------------------------------------------------------------------- 1 | 0 1 0 16 16 0 0 3 2 | 9 0 11 0 0 0 0 0 3 | 3 0 1 0 0 16 0 13 4 | 4 15 4 0 0 0 16 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0248.1.pfm: -------------------------------------------------------------------------------- 1 | 4 1 16 16 0 1 2 2 | 2 0 0 0 0 0 0 3 | 1 0 0 0 2 7 13 4 | 9 15 0 0 14 8 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0249.1.pfm: -------------------------------------------------------------------------------- 1 | 1 3 1 0 11 0 7 0 0 1 1 2 2 | 4 7 3 14 3 4 1 0 0 0 2 3 3 | 3 3 10 1 1 1 5 0 12 2 2 8 4 | 7 2 1 0 0 10 2 15 3 12 10 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0250.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 21 21 0 1 6 2 | 5 0 0 0 0 0 1 3 | 2 0 0 0 0 0 14 4 | 13 21 0 0 21 20 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0251.1.pfm: -------------------------------------------------------------------------------- 1 | 1 1 21 21 0 0 14 2 | 6 0 0 0 0 0 0 3 | 4 0 0 0 0 2 7 4 | 10 20 0 0 21 19 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0252.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 22 0 22 2 2 | 0 0 0 22 0 4 3 | 0 22 0 0 0 8 4 | 22 0 0 0 0 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0253.1.pfm: -------------------------------------------------------------------------------- 1 | 4 1 0 0 19 19 0 2 9 2 | 0 8 0 15 0 0 0 0 0 3 | 2 1 0 2 0 0 19 0 10 4 | 13 9 19 2 0 0 0 17 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0254.1.pfm: -------------------------------------------------------------------------------- 1 | 0 11 2 0 3 11 2 | 2 0 2 0 8 0 3 | 0 0 0 6 0 0 4 | 9 0 7 5 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0255.1.pfm: -------------------------------------------------------------------------------- 1 | 11 1 1 41 1 8 2 18 10 14 2 | 3 7 0 0 0 10 6 7 5 6 3 | 5 3 40 0 40 0 29 11 12 2 4 | 22 30 0 0 0 23 4 5 14 19 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0268.1.pfm: -------------------------------------------------------------------------------- 1 | 41 0 0 0 0 64 34 2 | 24 100 85 100 100 6 51 3 | 13 0 0 0 0 20 6 4 | 22 0 15 0 0 10 9 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0269.1.pfm: -------------------------------------------------------------------------------- 1 | 106 155 362 179 426 136 716 145 34 160 10 961 8 25 19 181 265 287 276 123 154 2 | 205 249 197 396 231 78 25 31 47 10 966 9 972 955 740 257 252 155 180 225 236 3 | 231 220 221 222 154 142 31 288 39 812 11 15 9 2 13 494 241 183 68 357 458 4 | 456 374 218 200 187 641 226 535 878 16 10 14 10 16 225 65 240 373 474 292 150 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0270.1.pfm: 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330 126 407 390 310 83 40 5 5 1 1 15 670 690 105 269 353 257 236 278 2 | 155 193 232 253 193 198 154 744 231 987 22 5 359 4 68 222 119 210 217 103 252 3 | 531 301 317 203 229 135 336 30 8 1 975 990 295 6 60 372 193 205 178 349 170 4 | 210 174 323 136 186 355 426 185 753 5 1 2 329 318 181 299 418 230 347 310 298 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0274.1.pfm: -------------------------------------------------------------------------------- 1 | 160 24 30 0 73 129 137 11 2 | 0 75 70 0 0 41 0 0 3 | 0 29 0 0 161 12 29 24 4 | 0 73 87 161 0 0 3 129 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0275.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 72 53 2 | 76 100 0 0 11 0 3 | 0 0 100 100 16 0 4 | 24 0 0 0 0 47 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0276.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 61 58 130 0 33 80 0 0 2 | 220 291 21 54 0 11 150 0 8 0 3 | 8 0 133 101 54 8 8 92 249 256 4 | 35 3 10 12 0 147 35 26 19 18 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0277.1.pfm: -------------------------------------------------------------------------------- 1 | 63 100 100 88 75 0 78 81 63 2 | 13 0 0 13 0 0 16 6 13 3 | 13 0 0 0 25 100 3 6 13 4 | 13 0 0 0 0 0 3 6 13 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0278.1.pfm: -------------------------------------------------------------------------------- 1 | 64 104 484 78 455 248 98 52 348 12 966 26 9 47 892 487 288 373 178 402 435 2 | 217 552 111 401 51 34 724 918 346 3 5 6 10 930 42 123 140 110 367 140 229 3 | 425 150 114 186 370 670 143 7 280 977 23 962 4 7 16 320 317 81 184 341 241 4 | 292 192 288 333 122 46 33 20 24 6 4 4 975 15 49 68 254 434 268 114 94 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0279.1.pfm: -------------------------------------------------------------------------------- 1 | 2056 97 0 1889 602 0 1947 2154 0 0 2 | 100 0 0 98 213 0 206 0 0 2088 3 | 98 0 0 0 1464 0 0 0 1416 0 4 | 0 2095 2154 172 0 2154 0 0 798 97 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0280.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 66 32 2 | 100 100 0 0 13 18 3 | 0 0 100 100 21 28 4 | 0 0 0 0 0 22 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0281.1.pfm: -------------------------------------------------------------------------------- 1 | 19 3 100 0 0 0 0 72 2 | 8 92 0 100 0 0 0 17 3 | 53 3 0 0 100 0 100 6 4 | 19 3 0 0 0 100 0 6 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0282.1.pfm: -------------------------------------------------------------------------------- 1 | 4 0 0 0 0 91 92 42 2 | 56 0 100 0 0 1 3 21 3 | 4 0 0 100 100 1 3 21 4 | 36 100 0 0 0 7 3 16 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0283.1.pfm: -------------------------------------------------------------------------------- 1 | 22 0 0 0 0 71 22 48 2 | 5 0 100 0 0 0 1 10 3 | 68 100 0 100 100 28 76 10 4 | 5 0 0 0 0 0 1 31 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0284.1.pfm: -------------------------------------------------------------------------------- 1 | 0 13 100 11 20 0 91 100 2 15 2 | 0 7 0 54 16 0 9 0 14 70 3 | 9 23 0 5 57 0 0 0 38 8 4 | 91 56 0 31 7 100 0 0 47 7 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0285.1.pfm: -------------------------------------------------------------------------------- 1 | 20 28 37 63 0 0 0 42 7 2 | 48 22 30 36 0 100 99 30 76 3 | 18 17 22 1 100 0 0 7 8 4 | 14 32 11 1 0 0 0 21 8 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0286.1.pfm: -------------------------------------------------------------------------------- 1 | 47 1 1 100 0 5 0 45 46 2 | 11 1 1 0 100 0 0 28 14 3 | 32 1 91 0 0 95 0 8 20 4 | 11 96 7 0 0 0 100 18 20 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0287.1.pfm: -------------------------------------------------------------------------------- 1 | 0 9 0 2 6 4 9 9 7 4 2 2 | 7 0 0 7 0 1 0 0 0 0 0 3 | 0 0 9 0 3 4 0 0 2 0 7 4 | 2 0 0 0 0 0 0 0 0 5 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0288.1.pfm: -------------------------------------------------------------------------------- 1 | 7 0 84 1 91 0 75 40 39 2 | 10 0 0 99 0 64 15 0 13 3 | 3 100 9 0 9 9 0 0 3 4 | 79 0 7 0 0 27 10 60 45 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0289.1.pfm: -------------------------------------------------------------------------------- 1 | 11 0 100 0 100 90 3 2 | 67 0 0 0 0 1 19 3 | 6 100 0 0 0 1 75 4 | 17 0 0 100 0 7 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0290.1.pfm: -------------------------------------------------------------------------------- 1 | 203 203 203 203 0 0 0 0 0 0 0 0 0 0 0 0 203 0 0 2 | 0 0 0 0 0 203 203 0 203 0 0 0 203 0 0 0 0 0 0 3 | 0 0 0 0 203 0 0 203 0 203 203 203 0 203 203 203 0 0 0 4 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 203 203 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0291.1.pfm: -------------------------------------------------------------------------------- 1 | 56 53 39 26 0 0 0 0 11 2 | 14 11 3 11 26 0 100 0 68 3 | 14 5 3 42 0 100 0 100 11 4 | 14 32 55 21 74 0 0 0 11 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0292.1.pfm: -------------------------------------------------------------------------------- 1 | 28 14 0 0 0 0 93 2 | 36 7 100 100 14 0 0 3 | 7 7 0 0 86 86 7 4 | 28 71 0 0 0 14 0 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0299.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 778 292 1019 2339 567 1913 659 96 1170 0 235 0 2 | 2779 0 438 655 1137 810 0 1296 335 592 767 517 1437 392 2779 3 | 0 2779 2273 927 1151 1002 538 810 0 1744 494 1105 729 419 0 4 | 0 0 97 717 498 390 98 194 737 204 1786 404 824 2001 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0300.1.pfm: -------------------------------------------------------------------------------- 1 | 13 17 0 100 0 100 100 3 2 | 44 42 0 0 0 0 0 9 3 | 19 5 100 0 0 0 0 84 4 | 25 36 0 0 100 0 0 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0301.1.pfm: -------------------------------------------------------------------------------- 1 | 65 8 92 12 3 6 51 28 32 2 | 9 2 0 0 94 27 19 33 25 3 | 20 88 0 1 1 4 18 21 21 4 | 6 1 8 87 2 63 12 17 21 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0302.1.pfm: -------------------------------------------------------------------------------- 1 | 36 31 80 3 98 0 0 5 40 28 33 2 | 21 26 4 0 0 0 99 28 20 26 24 3 | 24 18 12 96 0 0 0 3 23 23 21 4 | 20 26 4 0 2 99 0 64 17 22 21 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0303.1.pfm: -------------------------------------------------------------------------------- 1 | 218 371 362 282 275 169 535 11 2 968 2 13 57 973 15 376 207 284 226 254 337 2 | 295 217 213 119 177 140 35 8 5 13 433 4 934 6 413 290 354 216 234 329 169 3 | 245 268 150 325 316 365 413 6 934 4 562 13 5 8 35 131 194 202 177 232 195 4 | 240 142 273 272 230 325 15 973 57 13 1 968 2 11 535 202 244 296 361 183 297 5 | 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4 1 0 0 0 2 11 4 | 8 61 1 0 0 13 2 14 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0318.1.pfm: -------------------------------------------------------------------------------- 1 | 6 54 4 0 0 93 88 40 2 | 67 0 0 0 0 0 2 8 3 | 6 46 0 100 0 0 2 8 4 | 21 0 96 0 100 7 9 44 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0319.1.pfm: -------------------------------------------------------------------------------- 1 | 69 2 19 0 100 100 6 48 2 | 13 2 0 0 0 0 56 11 3 | 13 2 81 100 0 0 19 23 4 | 6 95 0 0 0 0 19 17 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0320.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 0 0 161 16 2 | 301 232 0 301 189 0 0 0 3 | 0 61 301 0 75 301 0 266 4 | 0 0 0 0 15 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0321.1.pfm: -------------------------------------------------------------------------------- 1 | 18 0 155 0 7 8 0 141 134 2 | 29 275 7 25 0 0 34 16 2 3 | 198 0 0 0 258 11 241 23 5 4 | 4 0 4 150 0 147 0 0 24 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0322.1.pfm: -------------------------------------------------------------------------------- 1 | 29 0 138 0 10 0 17 146 142 2 | 46 236 14 0 0 0 0 7 7 3 | 162 0 0 0 256 0 241 23 26 4 | 5 19 17 168 0 167 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0323.1.pfm: -------------------------------------------------------------------------------- 1 | 161 121 68 28 59 59 28 121 121 0 0 28 6 0 0 2 | 0 0 0 228 187 0 0 0 0 0 301 0 0 0 0 3 | 0 0 112 0 0 187 169 71 0 301 0 244 285 112 244 4 | 0 37 28 6 0 0 37 0 37 0 0 0 0 99 28 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0324.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 20 26 47 0 0 0 0 2 | 100 100 0 0 34 12 61 100 0 32 3 | 0 0 56 35 0 16 39 0 100 68 4 | 0 0 43 45 41 25 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0325.1.pfm: -------------------------------------------------------------------------------- 1 | 21 4 0 0 100 100 6 13 2 | 49 82 0 0 0 0 0 13 3 | 21 10 100 100 0 0 0 7 4 | 10 4 0 0 0 0 94 68 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0326.1.pfm: -------------------------------------------------------------------------------- 1 | 108 89 0 115 0 0 0 958 2 | 0 0 0 0 1714 0 1714 0 3 | 0 219 0 1599 0 0 0 655 4 | 1632 1451 1714 0 0 1714 0 113 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0327.1.pfm: -------------------------------------------------------------------------------- 1 | 101 0 203 0 203 203 0 2 | 0 203 0 203 0 0 0 3 | 101 0 0 0 0 0 0 4 | 0 0 0 0 0 0 203 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0328.1.pfm: -------------------------------------------------------------------------------- 1 | 0 9 0 0 0 10 9 4 0 2 | 10 0 0 0 0 0 1 0 0 3 | 0 2 0 11 0 0 0 0 0 4 | 1 0 11 0 11 1 1 7 11 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0329.1.pfm: -------------------------------------------------------------------------------- 1 | 55 0 15 0 0 35 33 2 | 10 100 0 88 2 17 30 3 | 18 0 85 0 98 9 18 4 | 17 0 0 12 0 39 18 5 | 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-------------------------------------------------------------------------------- 1 | 0 0 0 0 0 0 2 | 203 0 0 0 0 0 3 | 0 0 203 0 203 203 4 | 0 203 0 203 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0333.1.pfm: -------------------------------------------------------------------------------- 1 | 38 20 14 0 0 0 0 0 10 2 | 10 28 14 0 0 0 0 100 0 3 | 38 30 18 100 0 100 100 0 69 4 | 15 20 55 0 100 0 0 0 20 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0334.1.pfm: -------------------------------------------------------------------------------- 1 | 34 11 0 0 93 0 64 2 | 46 5 99 100 3 99 15 3 | 10 77 0 0 0 0 12 4 | 10 7 0 0 3 1 9 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0335.1.pfm: -------------------------------------------------------------------------------- 1 | 161 106 0 0 0 0 0 0 2 | 0 47 199 0 0 0 0 0 3 | 0 48 0 0 301 0 301 301 4 | 0 0 51 161 0 161 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0336.1.pfm: -------------------------------------------------------------------------------- 1 | 384 305 240 367 252 116 787 192 701 5 990 990 12 844 68 203 301 291 441 440 342 2 | 91 124 268 171 280 204 3 110 197 2 2 2 815 39 505 180 353 268 70 168 295 3 | 206 376 318 306 194 230 198 166 98 989 3 2 15 82 70 195 84 97 229 105 216 4 | 317 194 172 154 273 448 11 531 2 2 2 5 156 32 355 419 260 342 257 285 144 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0337.1.pfm: -------------------------------------------------------------------------------- 1 | 32 1 0 0 0 46 5 2 | 35 97 100 100 100 3 57 3 | 15 1 0 0 0 50 30 4 | 18 1 0 0 0 1 7 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0338.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 0 0 36 5 36 2 | 96 100 100 100 11 77 24 3 | 2 0 0 0 52 13 24 4 | 1 0 0 0 1 6 15 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0339.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 0 0 41 5 41 2 | 98 94 100 100 2 69 22 3 | 1 0 0 0 55 17 23 4 | 1 6 0 0 1 9 14 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0340.1.pfm: -------------------------------------------------------------------------------- 1 | 67 203 0 0 0 203 2 | 67 0 0 0 101 0 3 | 0 0 203 203 0 0 4 | 67 0 0 0 101 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0341.1.pfm: -------------------------------------------------------------------------------- 1 | 60 0 0 0 0 2 | 7 0 0 0 0 3 | 32 100 100 100 100 4 | 0 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0342.1.pfm: -------------------------------------------------------------------------------- 1 | 83 0 0 0 0 2 | 0 0 0 0 0 3 | 16 99 99 99 99 4 | 0 0 0 0 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0343.1.pfm: -------------------------------------------------------------------------------- 1 | 289 197 169 215 201 99 188 444 12 940 18 965 970 945 713 496 123 127 314 360 477 2 | 282 276 213 403 430 114 20 483 948 7 967 4 5 3 24 178 630 329 330 177 192 3 | 118 160 172 140 176 495 675 41 4 45 6 9 15 14 236 82 95 440 277 230 174 4 | 309 364 443 239 191 290 116 30 34 6 6 20 8 37 24 241 149 102 78 231 154 5 | 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266 226 278 288 203 98 1 921 3 21 978 18 57 22 135 376 421 308 327 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0351.1.pfm: -------------------------------------------------------------------------------- 1 | 278 194 156 131 239 141 516 79 29 6 1 972 1 0 36 223 280 188 163 153 185 2 | 135 250 332 249 85 480 59 420 770 52 990 0 0 968 9 575 265 298 435 371 149 3 | 231 266 223 268 400 145 138 392 197 83 4 1 27 1 876 177 252 72 208 183 202 4 | 354 289 287 351 273 232 285 107 3 858 2 25 969 28 78 22 202 441 192 290 462 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0352.1.pfm: -------------------------------------------------------------------------------- 1 | 8 0 0 13 2 8 10 62 2 | 28 100 100 0 88 2 3 8 3 | 15 0 0 87 8 88 83 22 4 | 48 0 0 0 2 2 3 8 5 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | 52 12 100 56 23 63 2 | 0 0 0 0 0 0 3 | 8 0 0 0 0 0 4 | 41 88 0 44 77 37 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0357.1.pfm: -------------------------------------------------------------------------------- 1 | 94 97 967 0 85 2 1 4 2 | 393 900 1 911 1 28 0 507 3 | 507 0 28 1 911 1 900 393 4 | 4 1 2 85 0 967 97 94 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0358.1.pfm: -------------------------------------------------------------------------------- 1 | 9 2 0 0 0 0 52 46 2 | 72 90 100 0 0 0 15 13 3 | 9 2 0 100 100 100 19 17 4 | 9 6 0 0 0 0 15 25 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0359.1.pfm: -------------------------------------------------------------------------------- 1 | 18 98 1 1 1 71 17 72 1 86 2 | 69 0 75 97 90 0 11 0 98 13 3 | 12 0 0 1 0 27 8 14 0 0 4 | 1 1 23 1 9 2 65 14 1 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0360.1.pfm: -------------------------------------------------------------------------------- 1 | 25 0 0 0 0 100 86 27 2 | 11 0 100 0 0 0 0 48 3 | 11 100 0 100 100 0 0 13 4 | 54 0 0 0 0 0 14 13 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0361.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 0 0 0 0 32 2 | 91 11 0 84 95 11 32 3 | 1 89 100 16 5 89 32 4 | 7 0 0 0 0 0 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0362.1.pfm: -------------------------------------------------------------------------------- 1 | 34 0 0 0 0 12 17 2 | 39 0 100 0 0 1 7 3 | 18 0 0 100 100 86 70 4 | 8 100 0 0 0 1 7 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0363.1.pfm: -------------------------------------------------------------------------------- 1 | 30 0 0 100 0 0 0 0 15 2 | 10 0 0 0 100 100 100 0 15 3 | 50 0 0 0 0 0 0 60 55 4 | 10 100 100 0 0 0 0 40 15 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0364.1.pfm: -------------------------------------------------------------------------------- 1 | 0 5 0 0 0 0 56 2 | 95 95 100 100 0 0 8 3 | 0 0 0 0 0 95 23 4 | 5 0 0 0 100 5 13 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0365.1.pfm: -------------------------------------------------------------------------------- 1 | 12 0 0 0 31 0 2 88 2 | 27 0 0 0 0 100 48 4 3 | 42 100 0 0 69 0 2 4 4 | 19 0 100 100 0 0 48 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0366.1.pfm: -------------------------------------------------------------------------------- 1 | 100 0 0 0 11 2 | 0 0 0 0 12 3 | 0 100 100 100 77 4 | 0 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0367.1.pfm: -------------------------------------------------------------------------------- 1 | 42 34 37 22 27 30 0 0 0 4 32 2 | 13 10 0 2 15 18 12 100 100 0 13 3 | 23 34 0 0 17 4 0 0 0 89 33 4 | 22 22 63 77 41 48 88 0 0 8 22 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0368.1.pfm: -------------------------------------------------------------------------------- 1 | 9 0 0 0 100 100 0 2 | 43 0 100 100 0 0 0 3 | 9 100 0 0 0 0 100 4 | 39 0 0 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0369.1.pfm: -------------------------------------------------------------------------------- 1 | 10 14 11 0 0 0 42 16 22 23 32 0 42 0 27 4 7 10 2 | 10 2 0 0 42 0 0 0 0 0 0 0 0 0 14 15 16 13 3 | 10 16 1 5 0 0 0 0 0 0 0 0 0 42 0 2 3 10 4 | 8 10 30 37 0 42 0 26 20 19 10 42 0 0 1 20 16 7 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0370.1.pfm: -------------------------------------------------------------------------------- 1 | 0 16 16 160 119 139 27 34 92 126 2 | 52 96 100 0 0 29 0 0 39 0 3 | 0 33 49 0 27 0 244 229 35 19 4 | 131 69 58 0 22 2 0 0 22 18 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0371.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 2 7 0 0 0 0 0 0 1 0 2 | 4 6 4 1 0 0 0 0 0 5 0 5 3 | 0 0 0 0 0 1 8 0 0 1 1 2 4 | 4 2 2 0 8 7 0 8 8 2 6 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0372.1.pfm: -------------------------------------------------------------------------------- 1 | 53 0 0 0 0 0 63 74 2 | 14 100 100 100 100 0 1 7 3 | 14 0 0 0 0 0 7 7 4 | 19 0 0 0 0 100 28 13 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0373.1.pfm: -------------------------------------------------------------------------------- 1 | 23 0 0 0 0 0 13 2 | 0 0 0 0 0 100 0 3 | 67 100 12 100 100 0 87 4 | 9 0 88 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0374.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 6 19 23 2 | 91 0 99 0 55 30 26 3 | 5 99 0 99 18 37 34 4 | 4 0 0 0 20 14 18 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0375.1.pfm: -------------------------------------------------------------------------------- 1 | 19 15 0 0 0 0 0 0 2 | 50 38 92 8 92 0 85 31 3 | 19 46 8 92 8 100 15 69 4 | 12 0 0 0 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0376.1.pfm: -------------------------------------------------------------------------------- 1 | 393 220 357 164 156 534 34 19 905 5 28 7 7 275 152 111 398 275 323 249 2 | 145 147 322 176 121 113 27 953 5 949 16 81 19 662 332 270 122 257 165 396 3 | 330 267 207 295 250 203 662 19 81 16 949 5 953 27 156 187 276 296 33 108 4 | 130 364 112 363 472 148 275 7 7 28 5 905 19 34 358 430 202 171 477 245 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0377.1.pfm: -------------------------------------------------------------------------------- 1 | 272 368 281 382 314 368 727 127 506 18 956 959 22 616 596 535 256 492 431 369 409 2 | 183 262 244 256 98 221 30 178 261 10 16 9 47 129 134 221 156 96 67 123 121 3 | 130 124 332 117 349 198 124 108 226 960 5 21 806 218 36 48 146 217 99 146 72 4 | 414 244 141 244 237 212 118 586 6 10 21 9 123 36 232 194 440 193 401 360 395 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0378.1.pfm: -------------------------------------------------------------------------------- 1 | 427 202 289 250 353 533 782 898 904 855 541 86 35 18 73 126 82 327 115 217 216 2 | 159 293 174 217 77 42 73 36 9 14 34 42 50 46 71 405 354 201 428 83 169 3 | 161 194 192 293 297 342 71 46 50 42 16 14 9 36 73 91 103 165 154 374 405 4 | 250 309 343 238 271 82 73 18 35 86 408 855 904 898 782 376 459 306 301 324 208 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0379.1.pfm: -------------------------------------------------------------------------------- 1 | 93 0 99 0 99 2 | 2 0 0 0 0 3 | 0 0 0 0 0 4 | 5 99 0 99 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0380.1.pfm: -------------------------------------------------------------------------------- 1 | 8 0 0 0 0 23 57 2 | 48 27 99 100 0 0 16 3 | 13 0 0 0 100 63 25 4 | 32 73 1 0 0 14 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0381.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 0 49 21 2 | 0 0 100 84 15 18 3 | 100 100 0 16 37 28 4 | 0 0 0 0 0 32 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0382.1.pfm: -------------------------------------------------------------------------------- 1 | 957 0 100 0 957 592 0 0 2 | 0 957 0 0 0 0 0 0 3 | 0 0 897 0 0 0 0 957 4 | 0 0 0 957 0 364 957 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0383.1.pfm: -------------------------------------------------------------------------------- 1 | 111 189 569 85 179 130 408 97 750 865 97 77 634 495 637 197 174 525 156 249 336 2 | 244 188 97 554 623 147 128 234 125 18 18 46 33 41 85 262 275 104 290 381 172 3 | 235 265 137 158 47 85 112 33 46 18 18 125 234 60 147 146 271 101 455 201 229 4 | 409 356 196 201 149 637 350 634 77 97 865 750 97 402 130 393 279 269 97 168 261 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0384.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 1405 0 3120 7 0 0 8 168 944 2 | 89 0 269 0 0 0 3136 0 3072 2969 231 3 | 313 3136 1721 0 35 3130 0 3136 75 0 1666 4 | 2817 0 0 3136 0 0 0 0 0 0 589 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0385.1.pfm: -------------------------------------------------------------------------------- 1 | 50 15 41 4 4 4 97 5 17 28 30 2 | 19 49 47 1 1 91 1 5 21 32 23 3 | 16 18 9 4 94 1 1 50 52 22 23 4 | 16 18 3 91 1 4 1 40 10 18 23 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0386.1.pfm: -------------------------------------------------------------------------------- 1 | 277 337 253 160 545 115 287 332 907 12 981 38 970 44 883 186 264 137 266 350 248 2 | 250 191 345 200 139 98 198 110 7 7 2 1 2 4 10 62 122 380 228 176 193 3 | 386 147 88 154 154 701 266 27 25 23 4 5 6 3 24 94 129 369 384 172 270 4 | 84 323 313 484 160 84 247 529 59 955 12 954 20 947 81 657 483 112 121 301 286 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0387.1.pfm: -------------------------------------------------------------------------------- 1 | 97 66 0 4 130 120 83 0 161 122 2 | 0 44 0 0 0 23 66 0 0 0 3 | 3 12 0 0 54 46 60 105 0 69 4 | 57 58 161 152 0 0 2 102 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0388.1.pfm: -------------------------------------------------------------------------------- 1 | 95 160 143 134 1 0 108 157 2 | 0 0 0 0 36 138 37 0 3 | 119 0 22 0 0 67 18 6 4 | 0 0 2 23 135 46 16 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0389.1.pfm: -------------------------------------------------------------------------------- 1 | 66 6 97 13 0 4 46 24 2 | 9 2 0 0 99 19 30 42 3 | 19 90 0 2 0 3 13 18 4 | 6 2 3 85 0 74 11 16 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0390.1.pfm: -------------------------------------------------------------------------------- 1 | 98 166 182 194 507 547 776 499 99 53 10 13 0 3 965 150 129 166 308 233 226 2 | 168 173 415 379 59 120 35 27 11 5 4 0 64 990 7 587 120 326 253 170 182 3 | 546 202 57 107 189 151 71 33 2 1 2 15 20 2 25 84 137 200 125 315 296 4 | 185 457 343 318 243 181 116 440 886 939 982 970 915 4 2 177 613 306 312 280 293 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0391.1.pfm: -------------------------------------------------------------------------------- 1 | 9 0 0 0 0 100 75 2 | 43 0 100 0 0 0 1 3 | 9 0 0 100 100 0 1 4 | 39 100 0 0 0 0 23 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0392.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 23 23 19 6 96 2 | 99 0 0 19 23 25 12 1 3 | 0 99 99 26 47 12 6 1 4 | 0 0 0 32 8 45 76 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0393.1.pfm: -------------------------------------------------------------------------------- 1 | 0 4297 27122 25290 27887 98 15301 2 | 3261 0 0 167 0 27779 3002 3 | 96 24137 1278 2703 0 0 9387 4 | 25022 198 0 0 0 97 2275 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0394.1.pfm: -------------------------------------------------------------------------------- 1 | 4 49 0 0 12 0 4 4 2 | 82 0 279 0 0 279 0 94 3 | 33 192 0 266 255 0 119 70 4 | 87 0 0 4 0 0 87 57 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0395.1.pfm: -------------------------------------------------------------------------------- 1 | 180 288 438 276 126 238 113 34 2 0 1 8 14 618 86 218 326 231 158 342 2 | 258 242 193 209 405 111 11 647 5 849 866 13 520 12 433 312 240 427 237 265 3 | 175 293 211 176 143 567 829 5 987 148 128 948 4 338 139 359 205 161 344 122 4 | 385 174 157 336 325 81 45 312 4 1 3 29 460 30 341 109 227 179 259 268 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0396.1.pfm: -------------------------------------------------------------------------------- 1 | 25 18 0 100 0 0 0 0 45 2 | 9 42 0 0 0 100 0 64 17 3 | 48 21 0 0 100 0 100 18 19 4 | 18 19 100 0 0 0 0 18 20 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0397.1.pfm: -------------------------------------------------------------------------------- 1 | 19 40 0 100 0 0 0 0 54 2 | 11 28 0 0 0 100 0 73 15 3 | 56 24 0 0 100 0 100 17 16 4 | 15 7 100 0 0 0 0 10 15 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0398.1.pfm: -------------------------------------------------------------------------------- 1 | 50 52 62 100 0 8 24 28 15 2 | 14 8 2 0 0 0 0 5 15 3 | 14 8 2 0 0 0 0 5 11 4 | 22 32 34 0 100 92 76 61 59 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0399.1.pfm: -------------------------------------------------------------------------------- 1 | 23 48 0 8 0 49 44 2 | 142 5 266 61 46 35 14 3 | 36 185 0 188 226 151 170 4 | 29 0 0 1 0 0 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0400.1.pfm: -------------------------------------------------------------------------------- 1 | 333 225 269 354 248 522 940 971 0 1 2 1 2 789 523 375 338 279 163 281 2 | 232 206 218 200 216 85 6 0 709 16 992 984 1 16 80 252 214 204 253 136 3 | 112 264 277 100 153 287 12 11 287 0 1 12 993 168 257 154 168 209 252 244 4 | 321 303 233 345 381 104 40 16 2 981 2 1 2 24 137 217 279 306 330 338 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0401.1.pfm: -------------------------------------------------------------------------------- 1 | 62 0 15 0 0 100 94 62 2 | 8 100 0 100 0 0 2 8 3 | 15 0 85 0 100 0 2 8 4 | 15 0 0 0 0 0 2 23 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0402.1.pfm: -------------------------------------------------------------------------------- 1 | 8 0 0 0 0 0 4 25 2 | 8 0 100 0 0 0 4 25 3 | 23 100 0 0 100 100 27 10 4 | 62 0 0 100 0 0 65 40 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0403.1.pfm: -------------------------------------------------------------------------------- 1 | 61 46 15 0 0 0 75 38 2 | 11 11 84 100 100 1 8 19 3 | 12 35 1 0 0 0 11 27 4 | 16 8 1 0 0 99 5 17 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0404.1.pfm: -------------------------------------------------------------------------------- 1 | 12 3 2 75 20 0 0 8 2 | 78 3 2 8 13 100 100 8 3 | 5 90 95 8 13 0 0 75 4 | 5 3 2 8 53 0 0 8 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0405.1.pfm: -------------------------------------------------------------------------------- 1 | 5 0 0 0 50 0 60 15 2 | 5 100 0 40 0 80 0 20 3 | 75 0 100 60 50 20 10 5 4 | 15 0 0 0 0 0 30 60 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0406.1.pfm: -------------------------------------------------------------------------------- 1 | 52 0 100 5 0 0 0 10 2 | 7 95 0 0 0 91 68 47 3 | 34 5 0 0 0 9 0 15 4 | 7 0 0 95 100 0 32 28 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0407.1.pfm: -------------------------------------------------------------------------------- 1 | 103 0 680 1265 1265 0 0 71 438 921 1265 0 1265 813 129 2 | 0 0 573 0 0 1024 543 599 0 0 0 0 0 0 1068 3 | 1162 1265 0 0 0 0 0 571 0 0 0 1265 0 451 89 4 | 0 0 61 0 0 241 805 90 826 344 0 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0408.1.pfm: -------------------------------------------------------------------------------- 1 | 28 1 0 0 0 100 64 50 2 | 47 16 0 0 100 0 7 15 3 | 20 1 100 0 0 0 7 15 4 | 5 82 0 100 0 0 22 19 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0409.1.pfm: -------------------------------------------------------------------------------- 1 | 3 100 0 0 0 0 78 2 | 93 0 100 10 0 0 8 3 | 3 0 0 90 0 100 8 4 | 3 0 0 0 100 0 8 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0410.1.pfm: -------------------------------------------------------------------------------- 1 | 10 4 0 0 0 0 2 85 2 | 44 28 0 100 0 0 27 2 3 | 27 63 100 0 100 100 69 2 4 | 19 4 0 0 0 0 2 10 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0411.1.pfm: -------------------------------------------------------------------------------- 1 | 16 59 38 100 0 1 83 2 | 25 3 0 0 100 0 5 3 | 19 28 0 0 0 99 9 4 | 40 9 62 0 0 0 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0412.1.pfm: -------------------------------------------------------------------------------- 1 | 2 0 2 0 0 0 0 0 1 18 10 7 2 2 | 0 10 0 0 18 0 0 17 0 0 1 2 0 3 | 0 5 16 18 0 18 18 0 0 0 0 1 1 4 | 16 3 0 0 0 0 0 1 17 0 7 8 15 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0413.1.pfm: -------------------------------------------------------------------------------- 1 | 269 306 342 131 133 318 1 0 3 1 0 0 956 850 174 233 212 181 205 219 2 | 223 182 168 193 55 551 967 977 993 981 6 2 0 92 257 235 191 185 100 297 3 | 250 216 206 146 157 101 26 0 1 0 3 869 36 21 162 93 197 321 265 365 4 | 255 294 283 528 652 28 3 20 1 16 989 126 5 35 405 438 399 311 428 116 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0414.1.pfm: -------------------------------------------------------------------------------- 1 | 12 0 0 0 100 40 31 2 | 51 0 100 0 0 8 22 3 | 7 0 0 100 0 50 31 4 | 31 100 0 0 0 3 15 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0415.1.pfm: -------------------------------------------------------------------------------- 1 | 297 143 148 240 212 397 5 8 976 1 60 10 971 981 35 320 182 247 248 199 2 | 261 225 128 121 210 528 3 13 3 900 36 9 6 8 28 332 273 308 254 195 3 | 211 313 305 201 327 50 8 6 9 36 900 3 13 3 516 228 154 204 309 177 4 | 230 318 418 436 249 23 981 971 10 60 1 976 8 5 418 118 390 239 187 426 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0416.1.pfm: -------------------------------------------------------------------------------- 1 | 65 0 0 100 0 0 2 50 2 | 19 0 0 0 100 0 2 12 3 | 12 0 0 0 0 100 2 19 4 | 4 100 100 0 0 0 94 19 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0417.1.pfm: -------------------------------------------------------------------------------- 1 | 122 124 86 0 161 19 2 | 0 0 0 264 0 0 3 | 0 67 136 0 0 0 4 | 34 0 0 17 0 137 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0418.1.pfm: -------------------------------------------------------------------------------- 1 | 174 228 134 114 252 43 491 27 25 889 38 172 67 647 829 162 228 337 430 166 2 | 297 141 92 434 231 114 412 23 21 32 555 48 85 193 62 76 474 85 127 439 3 | 371 587 332 109 72 646 36 56 112 49 103 722 37 64 72 481 142 428 302 243 4 | 156 41 440 342 444 195 58 892 840 28 302 56 809 95 34 278 155 148 139 150 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0419.1.pfm: -------------------------------------------------------------------------------- 1 | 7195 195 0 10172 1260 0 7781 10507 98 2246 6606 2 | 2582 0 0 98 1168 97 2526 0 0 7759 1126 3 | 195 0 2132 97 8333 0 198 0 6311 509 2313 4 | 869 10410 8375 172 0 10436 0 0 4323 394 1229 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0420.1.pfm: -------------------------------------------------------------------------------- 1 | 51 6 0 0 0 100 100 4 2 | 10 47 100 0 0 0 0 63 3 | 22 6 0 100 100 0 0 4 4 | 16 41 0 0 0 0 0 28 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0421.1.pfm: -------------------------------------------------------------------------------- 1 | 174 0 0 1832 0 0 118 0 49 779 2 | 0 0 103 0 1832 1832 1739 0 0 841 3 | 274 40 0 0 0 0 0 1832 1784 117 4 | 1457 1817 1784 0 0 0 0 0 0 291 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0422.1.pfm: -------------------------------------------------------------------------------- 1 | 25 0 0 0 74 23 56 14 94 36 2 | 38 100 0 0 9 17 0 0 6 17 3 | 11 0 100 100 17 46 0 0 0 15 4 | 27 0 0 0 0 14 43 85 0 32 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0423.1.pfm: -------------------------------------------------------------------------------- 1 | 35 0 0 0 0 0 60 21 32 2 | 28 97 91 100 100 0 0 0 28 3 | 23 1 0 0 0 0 8 4 5 4 | 13 2 9 0 0 100 32 75 34 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0424.1.pfm: -------------------------------------------------------------------------------- 1 | 28 2 0 0 0 0 69 46 2 | 37 17 77 100 0 0 31 15 3 | 6 10 15 0 100 100 0 23 4 | 28 71 8 0 0 0 0 15 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0425.1.pfm: -------------------------------------------------------------------------------- 1 | 36 0 0 0 1 41 0 27 23 24 25 25 22 26 2 | 24 100 99 100 99 0 98 26 26 26 24 22 26 24 3 | 27 0 0 0 0 31 1 17 20 20 25 26 26 26 4 | 14 0 1 0 0 28 1 31 31 30 26 27 26 25 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0426.1.pfm: -------------------------------------------------------------------------------- 1 | 0 203 203 0 0 0 2 | 0 0 0 0 0 0 3 | 0 0 0 0 0 203 4 | 203 0 0 203 203 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0427.1.pfm: -------------------------------------------------------------------------------- 1 | 39 26 15 12 2 0 0 5 57 26 35 2 | 21 25 43 30 94 99 7 1 7 17 26 3 | 19 27 17 10 2 0 92 93 26 46 18 4 | 21 22 25 48 2 0 0 1 9 11 21 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0428.1.pfm: -------------------------------------------------------------------------------- 1 | 48 69 0 0 0 92 52 65 10 2 | 23 10 100 0 0 0 2 6 10 3 | 15 19 0 100 100 8 44 6 10 4 | 15 2 0 0 0 0 2 23 69 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0429.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 0 21 9 13 56 2 | 100 0 0 64 66 5 14 3 | 0 100 100 14 16 77 7 4 | 0 0 0 0 9 5 21 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0430.1.pfm: -------------------------------------------------------------------------------- 1 | 13 0 0 0 96 4 23 27 2 | 42 100 0 0 0 14 2 5 3 | 13 0 100 100 4 82 5 5 4 | 31 0 0 0 0 0 70 63 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0431.1.pfm: -------------------------------------------------------------------------------- 1 | 32 0 0 0 0 30 0 44 19 2 | 24 100 100 100 100 0 100 16 35 3 | 23 0 0 0 0 36 0 3 15 4 | 21 0 0 0 0 34 0 38 31 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0432.1.pfm: -------------------------------------------------------------------------------- 1 | 8 0 0 0 100 10 90 33 2 | 8 100 0 0 0 0 0 3 3 | 18 0 100 100 0 80 0 3 4 | 68 0 0 0 0 10 10 63 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0433.1.pfm: -------------------------------------------------------------------------------- 1 | 1 0 100 100 0 0 62 54 2 | 25 0 0 0 0 0 3 13 3 | 7 0 0 0 0 0 15 13 4 | 66 100 0 0 100 100 21 19 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0434.1.pfm: -------------------------------------------------------------------------------- 1 | 11 0 9 63 40 100 0 0 36 2 | 36 0 26 26 0 0 0 100 30 3 | 11 100 0 0 60 0 0 0 17 4 | 41 0 65 11 0 0 100 0 17 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0435.1.pfm: -------------------------------------------------------------------------------- 1 | 75 158 382 376 274 552 16 4 2 983 884 986 5 4 326 86 258 450 281 333 2 | 242 204 170 240 50 169 747 4 16 7 1 2 2 983 575 221 190 110 396 330 3 | 144 341 173 137 462 240 17 988 3 3 109 4 2 1 55 77 196 173 62 68 4 | 537 295 274 245 212 37 218 2 978 5 4 6 989 9 43 613 354 266 260 266 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0436.1.pfm: -------------------------------------------------------------------------------- 1 | 15 0 0 0 100 0 23 2 | 66 100 100 100 0 100 26 3 | 0 0 0 0 0 0 34 4 | 20 0 0 0 0 0 18 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0437.1.pfm: -------------------------------------------------------------------------------- 1 | 61 32 17 24 17 12 0 0 3 2 | 0 0 0 4 44 32 93 100 0 3 | 26 0 0 2 11 7 7 0 93 4 | 13 68 83 69 28 49 0 0 5 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0438.1.pfm: -------------------------------------------------------------------------------- 1 | 51 2 0 0 100 60 93 12 2 | 15 94 0 0 0 12 1 8 3 | 23 2 100 100 0 16 1 4 4 | 11 2 0 0 0 12 5 76 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0439.1.pfm: -------------------------------------------------------------------------------- 1 | 21 16 22 89 19 28 4 0 0 3 6 2 | 42 16 8 1 9 33 22 100 100 0 41 3 | 22 10 4 2 4 8 7 0 0 95 14 4 | 15 57 66 8 68 32 68 0 0 2 39 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0440.1.pfm: -------------------------------------------------------------------------------- 1 | 169 0 0 0 0 107 169 119 0 0 0 21 119 9 46 2 | 0 279 279 97 0 77 0 17 0 0 0 97 0 17 0 3 | 0 0 0 0 0 17 0 57 279 279 0 37 57 0 198 4 | 0 0 0 107 169 0 0 0 0 0 169 58 9 145 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0441.1.pfm: -------------------------------------------------------------------------------- 1 | 15 31 0 0 0 0 19 5 50 2 | 15 11 100 100 100 100 4 85 10 3 | 15 11 0 0 0 0 54 5 10 4 | 55 46 0 0 0 0 24 5 30 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0442.1.pfm: -------------------------------------------------------------------------------- 1 | 0 8 0 0 0 0 2 | 19 2 1 0 3 0 3 | 0 2 4 0 19 1 4 | 3 10 17 22 0 21 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0443.1.pfm: -------------------------------------------------------------------------------- 1 | 14 10 4 2 0 0 2 0 0 15 2 | 3 0 0 0 0 0 28 0 0 1 3 | 7 20 18 28 30 30 0 30 20 10 4 | 6 0 8 0 0 0 0 0 10 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0444.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 22 25 2 7 3 2 | 1 0 0 0 0 0 0 3 | 1 0 0 0 0 1 22 4 | 23 25 3 0 23 17 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0446.1.pfm: -------------------------------------------------------------------------------- 1 | 3 5 0 0 0 13 4 6 0 23 15 2 | 0 0 0 0 0 0 13 7 11 0 4 3 | 0 22 0 0 1 14 2 3 2 1 4 4 | 24 0 27 27 26 0 8 11 14 3 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0447.1.pfm: -------------------------------------------------------------------------------- 1 | 28 0 1 54 0 7 0 55 60 2 2 | 5 0 1 0 53 0 6 3 0 25 3 | 25 0 3 6 0 53 0 1 0 5 4 | 2 60 55 0 7 0 54 1 0 28 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0448.1.pfm: -------------------------------------------------------------------------------- 1 | 6 2 16 31 0 8 24 2 | 3 1 1 0 0 0 0 3 | 4 0 1 0 0 9 7 4 | 19 29 14 1 32 15 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0449.1.pfm: -------------------------------------------------------------------------------- 1 | 1 3 1 22 1 2 1 1 7 1 2 | 2 7 31 1 30 1 10 1 17 30 3 | 30 17 1 10 1 30 1 31 7 2 4 | 1 7 1 1 2 1 22 1 3 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0450.1.pfm: -------------------------------------------------------------------------------- 1 | 3 8 0 0 0 0 0 0 24 2 | 0 0 0 0 32 0 0 0 3 3 | 18 24 32 32 0 32 3 31 2 4 | 11 0 0 0 0 0 29 1 3 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0451.1.pfm: -------------------------------------------------------------------------------- 1 | 19 25 16 5 0 21 0 17 1 0 25 5 2 | 1 1 0 9 4 0 0 0 3 26 0 12 3 | 2 0 0 6 1 5 26 8 18 0 1 7 4 | 4 0 10 6 21 0 0 1 4 0 0 2 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0452.1.pfm: -------------------------------------------------------------------------------- 1 | 3 11 24 30 18 0 2 2 0 4 20 2 | 17 4 0 0 6 0 0 0 1 0 4 3 | 5 10 7 0 7 31 29 29 7 5 3 4 | 6 6 0 1 0 0 0 0 23 22 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0453.1.pfm: -------------------------------------------------------------------------------- 1 | 2 29 0 0 0 24 28 28 4 6 19 4 2 | 1 0 0 0 19 0 0 0 1 5 5 3 3 | 1 0 0 25 1 0 1 0 0 8 1 15 4 | 25 0 29 4 9 5 0 1 24 10 4 7 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0454.1.pfm: -------------------------------------------------------------------------------- 1 | 7 10 0 12 0 0 15 0 0 11 5 2 | 5 5 14 0 0 0 0 0 15 3 4 3 | 0 0 1 3 15 0 0 15 0 1 6 4 | 3 0 0 0 0 15 0 0 0 0 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0455.1.pfm: -------------------------------------------------------------------------------- 1 | 0 0 22 22 0 0 13 2 | 11 0 0 0 0 0 0 3 | 4 0 0 0 0 0 8 4 | 7 22 0 0 22 22 1 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0456.1.pfm: -------------------------------------------------------------------------------- 1 | 0 10 1 1 0 0 0 0 4 0 3 2 2 | 1 7 16 15 16 18 18 14 0 14 1 0 3 | 15 1 0 1 1 0 0 0 13 2 4 16 4 | 2 0 1 1 1 0 0 4 1 2 10 0 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0457.1.pfm: -------------------------------------------------------------------------------- 1 | 4 0 16 17 0 1 8 2 | 6 0 0 0 0 0 1 3 | 0 0 0 0 0 1 4 4 | 7 17 1 0 17 15 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0458.1.pfm: -------------------------------------------------------------------------------- 1 | 8 0 3 0 0 0 27 1 17 4 15 2 | 3 0 0 0 0 0 0 22 8 13 3 3 | 14 0 38 0 1 2 4 7 15 3 4 4 | 16 41 0 41 40 39 10 11 1 21 19 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0459.1.pfm: -------------------------------------------------------------------------------- 1 | 20 29 33 31 0 0 0 33 31 17 2 | 4 0 0 1 0 2 33 0 0 10 3 | 4 4 0 1 33 0 0 0 1 2 4 | 5 0 0 0 0 31 0 0 1 4 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/MA0460.1.pfm: -------------------------------------------------------------------------------- 1 | 10 22 0 0 22 0 21 22 1 2 | 8 0 0 0 0 5 0 0 5 3 | 3 0 22 22 0 0 0 0 3 4 | 1 0 0 0 0 17 1 0 13 5 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/README.txt: -------------------------------------------------------------------------------- 1 | # Obtained from: http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl 2 | # Downloaded entire DB. 3 | # Options for extracting: 4 | rm ../*.pwm 5 | cat matrix_list.txt | perl makeJASPAR.pl ## ALL MOTIFS. 6 | grep vertebrates matrix_list.txt | perl makeJASPAR.pl ## Just vertebrate motifs. 7 | grep insects matrix_list.txt | perl makeJASPAR.pl ## Just insect motifs. 8 | -------------------------------------------------------------------------------- /parse_motifs/jaspar/jaspar_raw/makeJASPAR.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | sub trim($) 4 | { 5 | my $string = shift; 6 | $string =~ s/^\s+//; 7 | $string =~ s/\s+$//; 8 | return $string; 9 | } 10 | 11 | 12 | while() { 13 | @names = split(/[\s\t]/); 14 | $tfname = $names[2]; 15 | $filename = $names[0]; 16 | open(PWMFILE, "<", "$filename.pfm"); 17 | open(PWMOUT, ">", "../$tfname.$filename.pwm"); 18 | 19 | @A = split(/[\s\t]+/, trim(readline(PWMFILE))); 20 | @C = split(/[\s\t]+/, trim(readline(PWMFILE))); 21 | @G = split(/[\s\t]+/, trim(readline(PWMFILE))); 22 | @T = split(/[\s\t]+/, trim(readline(PWMFILE))); 23 | 24 | my $nbases = scalar @A; 25 | print PWMOUT "#$tfname $nbases\n"; 26 | print PWMOUT "A\tC\tG\tT\n"; 27 | for($i = 0; $i < $nbases; $i++) { 28 | print PWMOUT "$A[$i]\t$C[$i]\t$G[$i]\t$T[$i]\n"; 29 | } 30 | close(PWMOUT); 31 | close(PWMFILE); 32 | } 33 | 34 | -------------------------------------------------------------------------------- /parse_motifs/jolma/makeMatrix.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | sub trim($) 4 | { 5 | my $string = shift; 6 | $string =~ s/^\s+//; 7 | $string =~ s/\s+$//; 8 | return $string; 9 | } 10 | 11 | open (TFDBFILE, ">@ARGV[0]/tf.tsv"); 12 | 13 | while() { 14 | $header = trim($_); 15 | print TFDBFILE "$header\n"; 16 | 17 | @head_split = split(/[\s\t]/, $header); 18 | open(PWMFILE, ">@ARGV[0]/$head_split[0].$head_split[5].pwm"); 19 | 20 | $line = trim(); 21 | @A = split(/[\s\t]/, $line); 22 | $line = trim(); 23 | @C = split(/[\s\t]/, $line); 24 | $line = trim(); 25 | @G = split(/[\s\t]/, $line); 26 | $line = trim(); 27 | @T = split(/[\s\t]/, $line); 28 | 29 | $n = @A; 30 | print PWMFILE "#$header\n"; 31 | for($i=0; $i<$n; $i++) { 32 | print PWMFILE "$A[$i]\t$C[$i]\t$G[$i]\t$T[$i]\n"; 33 | } 34 | close(PWMFILE); 35 | } 36 | close(TFDBFILE); 37 | -------------------------------------------------------------------------------- /parse_motifs/jolma/run.bsh: -------------------------------------------------------------------------------- 1 | rm tf.tsv *.pwm 2 | 3 | mkdir teal 4 | cat teal.txt | perl makeMatrix.pl teal 5 | 6 | mkdir orange 7 | cat orange.txt | perl makeMatrix.pl orange 8 | 9 | mkdir green 10 | cat green.txt | perl makeMatrix.pl green 11 | 12 | -------------------------------------------------------------------------------- /parse_motifs/neph/makeNeph.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | sub trim($) 4 | { 5 | my $string = shift; 6 | $string =~ s/^\s+//; 7 | $string =~ s/\s+$//; 8 | return $string; 9 | } 10 | 11 | while() { 12 | if(/UW/) { 13 | @head_split = split(/[\s\t]/); 14 | open(PWMFILE, ">$head_split[0].pwm"); 15 | print PWMFILE "#$head_split[0]\n"; 16 | print PWMFILE "A C G T\n"; 17 | } elsif(/^\s*$/) { 18 | close(PWMFILE); 19 | } else { 20 | print PWMFILE $_; 21 | } 22 | } 23 | 24 | -------------------------------------------------------------------------------- /parse_motifs/neph/readme.txt: -------------------------------------------------------------------------------- 1 | ## Motifs derived from de novo calls in the Neph et. al. ENCODE paper. 2 | wget ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/supplementary/integration_data_jan2011/byDataType/footprints/jan2011/de.novo.pwm 3 | mv de.novo.pwm neph.txt 4 | cat neph.txt | perl makeNeph.pl 5 | # 6 | # From the README: 7 | # 8 | #./jan2011/de.novo.pwm shows the 683 discovered de novo motifs within footprints 9 | # : these are positional weight matrices 10 | # : columns are A,C,G,T 11 | # 12 | 13 | -------------------------------------------------------------------------------- /parse_motifs/uniprobe/makeUNIPROBE.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | sub trim($) 4 | { 5 | my $string = shift; 6 | $string =~ s/^\s+//; 7 | $string =~ s/\s+$//; 8 | return $string; 9 | } 10 | 11 | 12 | while() { 13 | @names = split(/[\s\t+]/); 14 | my $lenNames = scalar @names; 15 | 16 | ## Get the TF name. 17 | if( $lenNames > 1 ) { 18 | $tfname = $names[1]; 19 | $iupac = $names[5]; 20 | } else { 21 | $tfname = $names[0]; 22 | ; 23 | } 24 | 25 | ## Get ATCG. 26 | @A = split(/[\s\t]+/, trim()); 27 | @C = split(/[\s\t]+/, trim()); 28 | @G = split(/[\s\t]+/, trim()); 29 | @T = split(/[\s\t]+/, trim()); 30 | 31 | my $nbases = scalar @A; 32 | print "#$tfname $iupac $nbases\n"; #PWMOUT 33 | print "A\tC\tG\tT\n"; 34 | for($i = 1; $i < $nbases; $i++) { 35 | print "$A[$i]\t$C[$i]\t$G[$i]\t$T[$i]\n"; 36 | } 37 | # close(PWMOUT); 38 | } 39 | 40 | -------------------------------------------------------------------------------- /parse_motifs/uniprobe/readme.txt: -------------------------------------------------------------------------------- 1 | ## Gets the data 2 | wget http://the_brain.bwh.harvard.edu/uniprobe/downloads/All/all_pwms.zip 3 | unzip all_pwms.zip 4 | 5 | for i in Cell08 Cell09 CR09 EMBO10 GD09 GR09 MMB08 NBT06 PNAS08 SCI09 6 | do 7 | 8 | done 9 | 10 | -------------------------------------------------------------------------------- /rtfbsdb-manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb-manual.pdf -------------------------------------------------------------------------------- /rtfbsdb-tutorial.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb-tutorial.pptx -------------------------------------------------------------------------------- /rtfbsdb-vignette.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb-vignette.pdf -------------------------------------------------------------------------------- /rtfbsdb/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: rtfbsdb 2 | Version: 0.4.5 3 | Date: 2018-12-11 4 | Title: An Integrated Framework for Transcription Factor Binding Site Analysis 5 | Author: Charles G. Danko , Zhong Wang, Andre L. Martins 6 | Maintainer: Zhong Wang 7 | Depends: R (>= 2.6) 8 | Imports: rphast, rtfbs, parallel, grid, cluster, methods, latticeExtra, lattice, apcluster, vioplot, tools 9 | LinkingTo: 10 | Suggests: RCurl, stringr, bigWig, MotifDb 11 | Description: This package finds the transcription factor binding sites within specified genome loci and estimate the enrichment between two case-control group of different genomic loci based on a scoring algorithm driven by a Hidden Markov model and the CisBP database (or other data source, such as Jaspar, Transfac). It clusters motifs with similar DNA sequence specificities and optionally integrates RNA-seq or PRO-seq data to restrict analyses to motifs recognized by TFs expressed in the cell type of interest. PDF report is provided for the motif clustering, tfbs scaning and enrichment test. 12 | License: GPL-3 13 | biocViews: Sequencing, Analysis 14 | LazyLoad: yes 15 | -------------------------------------------------------------------------------- /rtfbsdb/NAMESPACE: -------------------------------------------------------------------------------- 1 | import(rphast) 2 | import(rtfbs) 3 | import(parallel) 4 | import(grid) 5 | import(cluster) 6 | import(methods) 7 | import(lattice) 8 | import(latticeExtra) 9 | import(apcluster) 10 | import(vioplot) 11 | import(tools) 12 | 13 | exportClasses("tfbs") 14 | exportClasses("tfbs.db") 15 | exportClasses("CisBP.db") 16 | 17 | export(CisBP.download, CisBP.zipload, CisBP.extdata, CisBP.group, CisBP.getTFinformation) 18 | export(tfbs, tfbs.dirs, tfbs.createFromCisBP) 19 | 20 | export(tfbs.createFromMotifDb) 21 | 22 | exportMethods(tfbs.importMotifs) 23 | exportMethods(tfbs.clusterMotifs) 24 | exportMethods(tfbs.getExpression) 25 | exportMethods(tfbs.selectExpressedMotifs) 26 | exportMethods(tfbs.drawLogo) 27 | exportMethods(tfbs.drawLogosForClusters) 28 | exportMethods(tfbs.selectByRandom) 29 | exportMethods(tfbs.selectByGeneExp) 30 | exportMethods(tfbs.scanTFsite ) 31 | exportMethods(tfbs.enrichmentTest) 32 | export(tfbs.reportFinding) 33 | export(tfbs.reportEnrichment) 34 | export(tfbs.plotEnrichment) 35 | export(write.starchbed) 36 | 37 | S3method(print, tfbs.finding) 38 | S3method(summary, tfbs.finding) 39 | S3method(print, tfbs.enrichment) 40 | S3method(summary, tfbs.enrichment) 41 | -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/Drosophila_melanogaster_ver_2015_12_08.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb/inst/extdata/Drosophila_melanogaster_ver_2015_12_08.zip -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/GSM1480327_K562_PROseq_chr19_minus.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb/inst/extdata/GSM1480327_K562_PROseq_chr19_minus.bw -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/GSM1480327_K562_PROseq_chr19_plus.bw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb/inst/extdata/GSM1480327_K562_PROseq_chr19_plus.bw -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/Homo_sapiens_ver_2015_12_08.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb/inst/extdata/Homo_sapiens_ver_2015_12_08.zip -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/M3590_1.01.pwm: -------------------------------------------------------------------------------- 1 | Pos A C G T 2 | 1 0.285714285714286 0.285714285714286 0.428571428571429 0.0 3 | 2 0.142857142857143 0.285714285714286 0.428571428571429 0.142857142857143 4 | 3 0.285714285714286 0.0 0.428571428571429 0.285714285714286 5 | 4 0.0 0.285714285714286 0.571428571428571 0.142857142857143 6 | 5 0.142857142857143 0.571428571428571 0.0 0.285714285714286 7 | 6 0.0 0.428571428571429 0.428571428571429 0.142857142857143 8 | 7 0.0 0.0 0.714285714285714 0.285714285714286 9 | 8 0.0 0.714285714285714 0.142857142857143 0.142857142857143 10 | 9 0.0 0.285714285714286 0.142857142857143 0.571428571428571 11 | 10 0.571428571428571 0.285714285714286 0.0 0.142857142857143 12 | 11 0.0 0.571428571428571 0.0 0.428571428571429 13 | 12 0.142857142857143 0.142857142857143 0.428571428571429 0.285714285714286 14 | 13 0.0 1.0 0.0 0.0 15 | 14 0.571428571428571 0.142857142857143 0.0 0.285714285714286 16 | 15 0.285714285714286 0.142857142857143 0.142857142857143 0.428571428571429 17 | 16 0.0 0.857142857142857 0.142857142857143 0.0 18 | 17 0.428571428571429 0.285714285714286 0.285714285714286 0.0 19 | 18 0.142857142857143 0.285714285714286 0.285714285714286 0.285714285714286 20 | 19 0.0 0.0 0.0 1.0 21 | 20 0.0 0.0 1.0 0.0 22 | 21 0.285714285714286 0.571428571428571 0.142857142857143 0.0 23 | 22 0.142857142857143 0.285714285714286 0.428571428571429 0.142857142857143 24 | 23 0.0 0.571428571428571 0.0 0.428571428571429 25 | 24 0.142857142857143 0.428571428571429 0.142857142857143 0.285714285714286 26 | 25 0.285714285714286 0.142857142857143 0.142857142857143 0.428571428571429 27 | 26 0.142857142857143 0.428571428571429 0.285714285714286 0.142857142857143 28 | 27 0.142857142857143 0.0 0.714285714285714 0.142857142857143 29 | 28 0.428571428571429 0.285714285714286 0.285714285714286 0.0 30 | -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/M3591_1.01.pwm: -------------------------------------------------------------------------------- 1 | Pos A C G T 2 | 1 0.2 0.0 0.4 0.4 3 | 2 0.0 0.4 0.4 0.2 4 | 3 0.2 0.2 0.2 0.4 5 | 4 0.6 0.0 0.4 0.0 6 | 5 0.0 0.4 0.0 0.6 7 | 6 0.0 0.4 0.4 0.2 8 | 7 0.0 0.0 1.0 0.0 9 | 8 0.2 0.0 0.0 0.8 10 | 9 0.0 0.6 0.0 0.4 11 | 10 0.6 0.4 0.0 0.0 12 | 11 0.0 1.0 0.0 0.0 13 | 12 0.0 0.0 1.0 0.0 14 | 13 0.0 1.0 0.0 0.0 15 | 14 0.0 0.2 0.0 0.8 16 | 15 0.0 0.4 0.0 0.6 17 | 16 0.2 0.4 0.2 0.2 18 | 17 0.8 0.0 0.2 0.0 19 | 18 0.2 0.2 0.6 0.0 20 | 19 0.4 0.2 0.4 0.0 21 | 20 0.4 0.2 0.0 0.4 22 | 21 0.4 0.2 0.2 0.2 23 | 22 0.2 0.2 0.0 0.6 24 | 23 0.0 0.8 0.0 0.2 25 | 24 0.4 0.2 0.0 0.4 26 | 25 0.0 0.4 0.4 0.2 27 | 26 0.2 0.0 0.4 0.4 28 | 27 0.0 0.4 0.0 0.6 29 | 28 0.0 0.4 0.2 0.4 30 | -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/Mus_musculus_ver_2015_12_08.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb/inst/extdata/Mus_musculus_ver_2015_12_08.zip -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/chrom_info_mm10.tab: -------------------------------------------------------------------------------- 1 | chr1 195471971 2 | chr10 130694993 3 | chr11 122082543 4 | chr12 120129022 5 | chr13 120421639 6 | chr14 124902244 7 | chr15 104043685 8 | chr16 98207768 9 | chr17 94987271 10 | chr18 90702639 11 | chr19 61431566 12 | chr1_GL456210_random 169725 13 | chr1_GL456211_random 241735 14 | chr1_GL456212_random 153618 15 | chr1_GL456213_random 39340 16 | chr1_GL456221_random 206961 17 | chr2 182113224 18 | chr3 160039680 19 | chr4 156508116 20 | chr4_GL456216_random 66673 21 | chr4_JH584292_random 14945 22 | chr4_GL456350_random 227966 23 | chr4_JH584293_random 207968 24 | chr4_JH584294_random 191905 25 | chr4_JH584295_random 1976 26 | chr5 151834684 27 | chr5_JH584296_random 199368 28 | chr5_JH584297_random 205776 29 | chr5_JH584298_random 184189 30 | chr5_GL456354_random 195993 31 | chr5_JH584299_random 953012 32 | chr6 149736546 33 | chr7 145441459 34 | chr7_GL456219_random 175968 35 | chr8 129401213 36 | chr9 124595110 37 | chrM 16299 38 | chrX 171031299 39 | chrX_GL456233_random 336933 40 | chrY 91744698 41 | chrY_JH584300_random 182347 42 | chrY_JH584301_random 259875 43 | chrY_JH584302_random 155838 44 | chrY_JH584303_random 158099 45 | chrUn_GL456239 40056 46 | chrUn_GL456367 42057 47 | chrUn_GL456378 31602 48 | chrUn_GL456381 25871 49 | chrUn_GL456382 23158 50 | chrUn_GL456383 38659 51 | chrUn_GL456385 35240 52 | chrUn_GL456390 24668 53 | chrUn_GL456392 23629 54 | chrUn_GL456393 55711 55 | chrUn_GL456394 24323 56 | chrUn_GL456359 22974 57 | chrUn_GL456360 31704 58 | chrUn_GL456396 21240 59 | chrUn_GL456372 28664 60 | chrUn_GL456387 24685 61 | chrUn_GL456389 28772 62 | chrUn_GL456370 26764 63 | chrUn_GL456379 72385 64 | chrUn_GL456366 47073 65 | chrUn_GL456368 20208 66 | chrUn_JH584304 114452 67 | -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/fake_M2938_1.02.pwm: -------------------------------------------------------------------------------- 1 | Pos A C G T 2 | 1 0.2 0.0 0.4 0.4 3 | 2 0.0 0.4 0.4 0.2 4 | 3 0.2 0.2 0.2 0.4 5 | 4 0.6 0.0 0.4 0.0 6 | 5 0.0 0.4 0.0 0.6 7 | 6 0.0 0.4 0.4 0.2 8 | 7 0.0 0.0 1.0 0.0 9 | 8 0.2 0.0 0.0 0.8 10 | 9 0.0 0.6 0.0 0.4 11 | 10 0.6 0.4 0.0 0.0 12 | 11 0.0 1.0 0.0 0.0 13 | 12 0.0 0.0 1.0 0.0 14 | 13 0.0 1.0 0.0 0.0 15 | 14 0.0 0.2 0.0 0.8 16 | 15 0.0 0.4 0.0 0.6 17 | 16 0.2 0.4 0.2 0.2 18 | 17 0.8 0.0 0.2 0.0 19 | 18 0.2 0.2 0.6 0.0 20 | 19 0.4 0.2 0.4 0.0 21 | 20 0.4 0.2 0.0 0.4 22 | 21 0.4 0.2 0.2 0.2 23 | 22 0.2 0.2 0.0 0.6 24 | 23 0.0 0.8 0.0 0.2 25 | 24 0.4 0.2 0.0 0.4 26 | 25 0.0 0.4 0.4 0.2 27 | 26 0.2 0.0 0.4 0.4 28 | 27 0.0 0.4 0.0 0.6 29 | 28 0.0 0.4 0.2 0.4 30 | -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/fake_M2940_1.02.pwm: -------------------------------------------------------------------------------- 1 | Pos A C G T -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/gencode.v19.annotation.chr19.gtf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb/inst/extdata/gencode.v19.annotation.chr19.gtf.gz -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/hg19.chr19.2bit: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb/inst/extdata/hg19.chr19.2bit -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/human_PI_fastq_gz_sort_chr19.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb/inst/extdata/human_PI_fastq_gz_sort_chr19.bam -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/human_PI_fastq_gz_sort_chr19.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb/inst/extdata/human_PI_fastq_gz_sort_chr19.bam.bai -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/pwm.example.meme.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/rtfbsdb/inst/extdata/pwm.example.meme.txt -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/pwm.example.transfac.txt: -------------------------------------------------------------------------------- 1 | AC oligo-analysis.asmb_m1 2 | XX 3 | ID tin_like_motif 4 | XX 5 | DE vkcTCAAGTGgctw 6 | PO A C G T 7 | 1 12 10 10 5 8 | 2 5 7 13 12 9 | 3 2 24 6 5 10 | 4 1 0 0 36 11 | 5 0 36 0 1 12 | 6 36 0 1 0 13 | 7 37 0 0 0 14 | 8 0 1 36 0 15 | 9 0 0 0 37 16 | 10 0 0 36 1 17 | 11 5 6 22 4 18 | 12 4 19 7 7 19 | 13 8 8 6 15 20 | 14 10 4 8 15 21 | XX 22 | CC program: feature 23 | CC matrix.nb: 1 24 | CC matrix.nb: 1 25 | CC sites: 37 26 | CC consensus.strict: agcTCAAGTGgctt 27 | CC consensus.strict.rc: AAGCCACTTGAGCT 28 | CC consensus.IUPAC: vkcTCAAGTGgctw 29 | CC consensus.IUPAC.rc: WAGCCACTTGAGMB 30 | CC consensus.regexp: [acg][gt]cTCAAGTGgct[at] 31 | CC consensus.regexp.rc: [AT]AGCCACTTGAG[AC][CGT] 32 | XX 33 | // 34 | AC oligo-analysis.asmb_m2 35 | XX 36 | ID gata_like_motif 37 | XX 38 | DE wmmAGATACam 39 | PO A C G T 40 | 1 17 7 6 12 41 | 2 17 12 6 7 42 | 3 13 19 7 3 43 | 4 42 0 0 0 44 | 5 0 0 42 0 45 | 6 42 0 0 0 46 | 7 0 0 0 42 47 | 8 42 0 0 0 48 | 9 0 42 0 0 49 | 10 21 5 8 8 50 | 11 12 16 5 9 51 | XX 52 | CC program: feature 53 | CC matrix.nb: 2 54 | CC matrix.nb: 2 55 | CC sites: 42 56 | CC consensus.strict: aacAGATACac 57 | CC consensus.strict.rc: GTGTATCTGTT 58 | CC consensus.IUPAC: wmmAGATACam 59 | CC consensus.IUPAC.rc: KTGTATCTKKW 60 | CC consensus.regexp: [at][ac][ac]AGATACa[ac] 61 | CC consensus.regexp.rc: [GT]TGTATCT[GT][GT][AT] 62 | XX 63 | // 64 | -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/pwm.format.jaspar.txt: -------------------------------------------------------------------------------- 1 | ### Format demo 2 | #> Mycn 3 | #A [ 0 29 0 2 0 0 ] 4 | #C [31 0 30 1 3 0 ] 5 | #G [ 0 0 0 28 0 31] 6 | #T [ 0 2 1 0 28 0 ] 7 | 8 | >$Motif_ID $TF_Name 9 | A [ $A+ ] 10 | C [ $C+ ] 11 | G [ $G+ ] 12 | T [ $T+ ] 13 | -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/pwm.format.meme.txt: -------------------------------------------------------------------------------- 1 | ### Format demo 2 | # Background letter frequencies 3 | # A 0.303 C 0.183 G 0.209 T 0.306 4 | # 5 | # MOTIF crp alternative name 6 | # letter-probability matrix: alength= 4 w= 19 nsites= 17 E= 4.1e-009 7 | # 0.000000 0.176471 0.000000 0.823529 8 | # 0.000000 0.058824 0.647059 0.294118 9 | # 0.000000 0.058824 0.000000 0.941176 10 | # 0.176471 0.000000 0.764706 0.058824 11 | # 0.823529 0.058824 0.000000 0.117647 12 | # 0.294118 0.176471 0.176471 0.352941 13 | # 0.294118 0.352941 0.235294 0.117647 14 | # 0.117647 0.235294 0.352941 0.294118 15 | # 0.529412 0.000000 0.176471 0.294118 16 | # 0.058824 0.235294 0.588235 0.117647 17 | # 0.176471 0.235294 0.294118 0.294118 18 | # 0.000000 0.058824 0.117647 0.823529 19 | # 0.058824 0.882353 0.000000 0.058824 20 | # 0.764706 0.000000 0.176471 0.058824 21 | # 0.058824 0.882353 0.000000 0.058824 22 | # 0.823529 0.058824 0.058824 0.058824 23 | # 0.176471 0.411765 0.058824 0.352941 24 | # 0.411765 0.000000 0.000000 0.588235 25 | # 0.352941 0.058824 0.000000 0.588235 26 | 27 | 28 | MOTIF $Motif_ID $TF_Name $SKIP 29 | letter-probability matrix: $SKIP 30 | $A $C $G $T $REPEAT 31 | URL $SKIP 32 | -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/pwm.format.mscan.txt: -------------------------------------------------------------------------------- 1 | ### Format demo 2 | #>mef2 3 | #10 0 0 0 22 0 6 2 3 4 22 10 4 | #0 2 12 0 0 0 0 0 0 0 0 0 5 | #9 20 2 0 0 0 0 0 0 0 0 10 6 | #3 0 8 22 0 22 16 20 19 18 0 2 7 | 8 | >$Motif_ID $TF_Name $SKIP 9 | $A+ 10 | $C+ 11 | $G+ 12 | $T+ 13 | -------------------------------------------------------------------------------- /rtfbsdb/inst/extdata/pwm.format.transfac.txt: -------------------------------------------------------------------------------- 1 | ### Format demo 2 | #AC MA0001.1 3 | #XX 4 | #ID AGL3 5 | #XX 6 | #DE MA0001.1 AGL3; from JASPAR 7 | #PO A C G T 8 | #1 0 94 1 2 9 | #2 3 75 0 19 10 | #3 79 4 3 11 11 | #4 40 3 4 50 12 | #5 66 1 1 29 13 | #6 48 2 0 47 14 | #7 65 5 5 22 15 | #8 11 2 3 81 16 | #9 65 3 28 1 17 | #10 0 3 88 6 18 | #XX 19 | #CC program: jaspar 20 | #XX 21 | #// 22 | 23 | AC $Motif_ID 24 | XX $SKIP 25 | ID $TF_Name 26 | XX $SKIP 27 | DE $Description 28 | PO A C G T 29 | $LOM $A $C $G $T $REPEAT 30 | XX $SKIP 31 | CC $SKIP $REPEAT 32 | // $EOM -------------------------------------------------------------------------------- /rtfbsdb/man/CisBP.db.class.Rd: -------------------------------------------------------------------------------- 1 | \name{CisBP.db-class} 2 | \Rdversion{1.1} 3 | \docType{class} 4 | \alias{CisBP.db-class} 5 | \alias{tfbs.createFromCisBP,CisBP.db-method} 6 | \alias{CisBP.group,CisBP.db-method} 7 | \alias{CisBP.getTFinformation,CisBP.db-method} 8 | 9 | \title{Class \code{"CisBP.db"}} 10 | \description{ 11 | The motif library from CisBP web site.\cr 12 | Link: \code{http://cisbp.ccbr.utoronto.ca/} 13 | } 14 | \section{Objects from the Class}{ 15 | Objects can be created by calls of the form \code{\link{CisBP.extdata}}, \code{\link{CisBP.zipload}}, \code{\link{CisBP.download}}. 16 | } 17 | \section{Slots}{ 18 | \describe{ 19 | \item{\code{species}:}{String indicating the species name defined in the CisBP dataset.} 20 | \item{\code{zip.file}:}{String indicating the filename of temporary data file.} 21 | \item{\code{zip.url}:}{String indicating the download source.} 22 | \item{\code{zip.date}:}{String indicating the download date.} 23 | \item{\code{file.tfinfo}:}{String indicating the TF filename, defulat is TF_Information.txt.} 24 | } 25 | } 26 | \section{Extends}{ 27 | Class \code{"\linkS4class{tfbs.db}"}, directly. 28 | } 29 | \section{Methods}{ 30 | \describe{ 31 | \item{\link{tfbs.createFromCisBP}}{Build a tfbs object by querying the meta file of CisBP dataset and subsetting the results.} 32 | \item{\link{CisBP.group}}{Get the statistical summary by grouping the field in the CisBP dataset.} 33 | \item{\link{CisBP.getTFinformation}}{Get the TF Information stored in the CisBP dataset.} 34 | } 35 | } 36 | \references{ 37 | Weirauch, M. T., Yang, A., Albu, M., Cote, A. G., Montenegro-Montero, A., Drewe, P., ... & Hughes, T. R. (2014). Determination and inference of eukaryotic transcription factor sequence specificity. Cell, 158(6), 1431-1443. 38 | } 39 | 40 | \seealso{ 41 | \code{\link{CisBP.getTFinformation}}, \code{\link{CisBP.group}}, \code{\link{tfbs.createFromCisBP}} 42 | } 43 | \examples{ 44 | showClass("CisBP.db") 45 | } 46 | \keyword{classes} 47 | -------------------------------------------------------------------------------- /rtfbsdb/man/CisBP.download.Rd: -------------------------------------------------------------------------------- 1 | \name{CisBP.download} 2 | \alias{CisBP.download} 3 | \title{ Download CisBP dataset.} 4 | \description{ 5 | Download TF data file from CisBP dataset and store it to temporary folder 6 | } 7 | \usage{ 8 | CisBP.download(species = "Homo_sapiens", 9 | url = "http://cisbp.ccbr.utoronto.ca/bulk_archive.php") 10 | } 11 | \arguments{ 12 | \item{species}{ String, indicating the species name in the CisBP dataset } 13 | \item{url}{ String, the URL of bulk dowbnloads from CisBP dataset, \cr default is \code{http://cisbp.ccbr.utoronto.ca/bulk_archive.php}} 14 | } 15 | \details{ 16 | The dowload function has been confirmed in the web site of \emph{cisbp.ccbr.utoronto.ca} o June, 2015. 17 | } 18 | \value{ 19 | A CisBP object (class name: \code{"\linkS4class{CisBP.db}"}) is returned with four items: 20 | \item{species}{String indicating the species name} 21 | \item{zip.file}{String indicating the filename of temporary data file.} 22 | \item{zip.url}{String indicating the download source } 23 | \item{file.tfinfo}{String indicating the TF filename, default is TF_Information.txt.} 24 | } 25 | \references{ 26 | Weirauch, M. T., Yang, A., Albu, M., Cote, A. G., Montenegro-Montero, A., Drewe, P., ... & Hughes, T. R. (2014). Determination and inference of eukaryotic transcription factor sequence specificity. Cell, 158(6), 1431-1443. 27 | } 28 | 29 | \seealso{ 30 | See Also as \code{\link{CisBP.zipload}}, \code{\link{CisBP.extdata}}. 31 | } 32 | \examples{ 33 | 34 | #download zebra fish dataset 35 | db1 <- CisBP.download("Danio_rerio"); 36 | 37 | #download Felis_catus dataset 38 | db2 <- CisBP.download("Felis_catus"); 39 | 40 | } 41 | \keyword{CisBP object} 42 | 43 | -------------------------------------------------------------------------------- /rtfbsdb/man/CisBP.extdata.Rd: -------------------------------------------------------------------------------- 1 | \name{CisBP.extdata} 2 | \alias{CisBP.extdata} 3 | \title{ 4 | Load internal CisBP dataset. 5 | } 6 | \description{ 7 | Build a CisBP object from the internal zip file stored in this package 8 | } 9 | \usage{ 10 | CisBP.extdata(species) 11 | } 12 | \arguments{ 13 | \item{species}{ String, only valid for human and mouse species, i.e. Homo_sapiens, Mus_musculus, or Drosophila_melanogaster } 14 | } 15 | \details{ 16 | The CisBP data for Homo_sapiens and Mus_musculus are delivered by this package. When you use the newest dataset, you should download it from the website by \code{\link{CisBP.download}}. 17 | } 18 | \value{ 19 | A CisBP object (class name: \code{"\linkS4class{CisBP.db}"}) is returned with four items: 20 | \item{species}{String indicating the species name defined in the CisBP dataset.} 21 | \item{zip.file}{String indicating the filename of temporary data file.} 22 | \item{zip.url}{String indicating the download source } 23 | \item{file.tfinfo}{String indicating the TF filename, default is TF_Information.txt.} 24 | } 25 | 26 | \seealso{ 27 | See Also as \code{\link{CisBP.zipload}}, \code{\link{CisBP.download}}. 28 | } 29 | \examples{ 30 | 31 | #reading human data from extension data file in the package 32 | db.human <- CisBP.extdata("Homo_sapiens") 33 | 34 | #reading Drosophila_melanogaster from extension data file in the package 35 | db.dm3 <- CisBP.extdata("dm3") 36 | 37 | } 38 | \keyword{CisBP object} 39 | -------------------------------------------------------------------------------- /rtfbsdb/man/CisBP.group.Rd: -------------------------------------------------------------------------------- 1 | \name{CisBP.group} 2 | \alias{CisBP.group} 3 | \title{ 4 | Summarize the motif number. 5 | } 6 | \description{ 7 | Get the statistical summary by grouping the field in the CisBP dataset. 8 | } 9 | \usage{ 10 | CisBP.group(cisbp.db, 11 | group.by=c("tf_name", "tf_species", "tf_status", "family_name", 12 | "motif_type", "msource_id"), 13 | tf.information.type=NA ) 14 | } 15 | \arguments{ 16 | \item{cisbp.db}{ A CisBP object (\code{"\linkS4class{CisBP.db}"}) including the TF_Information.txt.} 17 | \item{group.by}{ String, indicating which field will be used to group values. Available values are tf_name, tf_species, tf_status, family_name, motif_type and msource_id.} 18 | \item{tf.information.type}{ Number, indicating which TF meta file will be used. Available values are 1 for \cr 19 | TF_Information.txt, 2 for TF_Information_all_motifs.txt and 3 \cr 20 | for F_Information_all_motifs_plus.txt.} 21 | } 22 | \details{ 23 | Three TF information files in CisBP dataset.\cr\cr 24 | 1: TF_Information.txt : (direct motifs) or (no direct but inferred motifs with 90\%)\cr 25 | 2: TF_Information_all_motifs.txt: (direct motifs) and (inferred motifs above the threshold)\cr 26 | 3: F_Information_all_motifs_plus.txt: All motifs\cr 27 | } 28 | \value{ 29 | A data frame returned includes two columns 30 | \item{group_by}{Values of grouping field} 31 | \item{number}{Counts of group value } 32 | } 33 | \seealso{ 34 | See Also as \code{\link{tfbs.createFromCisBP}} 35 | } 36 | \examples{ 37 | 38 | # Load the internal CisBP dataset 39 | db_human <- CisBP.extdata("Homo_sapiens"); 40 | 41 | # Group the motif count by the column of family_name in TF_Information.txt 42 | gr1 <- CisBP.group(db_human, group.by="family_name", tf.information.type=1 ); 43 | 44 | # Group the motif count by the column of tf_status in TF_Information.txt 45 | gr2 <- CisBP.group(db_human, group.by="tf_status", tf.information.type=1 ); 46 | 47 | # Group the motif count by the column of tf_status 48 | # in TF_Information_all_motifs.txt 49 | gr3 <- CisBP.group(db_human, group.by="tf_status", tf.information.type=2); 50 | 51 | # Group the motif count by the column of tf_status 52 | # in F_Information_all_motifs_plus.txt 53 | gr4 <- CisBP.group(db_human, group.by="tf_status", tf.information.type=3); 54 | 55 | } 56 | 57 | \keyword{CisBP object} 58 | -------------------------------------------------------------------------------- /rtfbsdb/man/CisBP.zipload.Rd: -------------------------------------------------------------------------------- 1 | \name{CisBP.zipload} 2 | \alias{CisBP.zipload} 3 | \title{ 4 | Load the zipped CisBP file. 5 | } 6 | \description{ 7 | Build a CisBP object from the zipped CisBP file. 8 | } 9 | \usage{ 10 | CisBP.zipload(zip.file, species) 11 | } 12 | \arguments{ 13 | \item{zip.file}{ String, indicating the zipped file data } 14 | \item{species}{ String, indicating the species name in the CisBP database } 15 | } 16 | \details{ 17 | The zip data canbe downloaded from the web site, please check \code{\link{CisBP.download}}. 18 | } 19 | 20 | \value{ 21 | A CisBP object (class name: \code{"\linkS4class{CisBP.db}"}) is returned with four items: 22 | \item{species}{String indicating the species name} 23 | \item{zip.file}{String indicating the filename of temporary data file.} 24 | \item{zip.url}{String indicating the download source } 25 | \item{file.tfinfo}{String indicating the TF filename, default is TF_Information.txt.} 26 | } 27 | \seealso{ 28 | See Also as \code{\link{CisBP.extdata}}, \code{\link{CisBP.download}}. 29 | } 30 | \examples{ 31 | 32 | # Download the dataset 33 | db1 <- CisBP.download("Arabidopsis_thaliana"); 34 | 35 | # Loading the zip file, the db2 and db3 have same TF data. 36 | # Here is an example to show how to use CisBP.zipload. 37 | # We dont nee to download it by CisBP.download and then load it 38 | # by CisBP.zipload 39 | db2 <- CisBP.zipload(db1@zip.file, species="Arabidopsis thaliana"); 40 | 41 | } 42 | \keyword{CisBP object} 43 | -------------------------------------------------------------------------------- /rtfbsdb/man/print.tfbs.enrichment.Rd: -------------------------------------------------------------------------------- 1 | \name{print.tfbs.enrichment} 2 | \alias{print.tfbs.enrichment} 3 | \title{ 4 | Print the brief enrichment results 5 | } 6 | \description{ 7 | Print the brief enrichment results. 8 | } 9 | \usage{ 10 | \method{print}{tfbs.enrichment}(x, \dots, pv.threshold=0.05, pv.adj=NA ) 11 | } 12 | \arguments{ 13 | \item{x}{The result obtained by \code{\link{tfbs.enrichmentTest}}.} 14 | \item{\dots}{Additional arguments affecting the print produced.} 15 | \item{pv.threshold}{Numeric value,indicating whether the different cutoff of p-value is applied to select the significant motifs. } 16 | \item{pv.adj}{String, P-values correct method for \code{p.adjust} function. The available values are "holm", \cr 17 | "hochberg", "hommel", "bonferroni", "BH", "BY","fdr" or "none".\cr 18 | (default="bonferroni").} 19 | } 20 | \details{ 21 | This command shows the calling parameters and significant motifs from the result object.\cr 22 | The significant motifs are selected by the corrected p-value cutoff(0.05) and at most 20 significant motifs are listed. 23 | The adjust method of p-value is defined in the calling function. 24 | } 25 | \value{ 26 | No return values. 27 | } 28 | 29 | \seealso{ 30 | See also as \code{\link{tfbs.enrichmentTest}}. 31 | } 32 | \examples{ 33 | #See example in tfbs.enrichmentTest 34 | } 35 | \keyword{print} 36 | \keyword{Enrichment} 37 | -------------------------------------------------------------------------------- /rtfbsdb/man/print.tfbs.finding.Rd: -------------------------------------------------------------------------------- 1 | \name{print.tfbs.finding} 2 | \alias{print.tfbs.finding} 3 | \title{ 4 | Print scanning result of TF sites. 5 | } 6 | \description{ 7 | Print scanning result of TF sites. 8 | } 9 | \usage{ 10 | \method{print}{tfbs.finding}(x, \dots) 11 | } 12 | \arguments{ 13 | \item{x}{The result obtained by \code{\link{tfbs.scanTFsite}}.} 14 | \item{\dots}{Additional arguments affecting the print produced.} 15 | } 16 | \details{ 17 | This function shows a brief information including calling parameters and enriched motifs. 18 | } 19 | \value{ 20 | No return values. 21 | } 22 | \seealso{ 23 | See Also as \code{\link{tfbs.scanTFsite}} 24 | } 25 | \examples{ 26 | #See example in tfbs.scanTFsite 27 | } 28 | \keyword{ print } 29 | \keyword{Scanning} 30 | -------------------------------------------------------------------------------- /rtfbsdb/man/summary.tfbs.enrichment.Rd: -------------------------------------------------------------------------------- 1 | \name{summary.tfbs.enrichment} 2 | \alias{summary.tfbs.enrichment} 3 | \title{ 4 | Summarize the enrichment result 5 | } 6 | \description{ 7 | Return the significant motifs based on the adjust p-values using multiple comparisons. 8 | } 9 | \usage{ 10 | \method{summary}{tfbs.enrichment}(object, pv.threshold = 0.05, pv.adj = NA, \dots) 11 | } 12 | 13 | \arguments{ 14 | \item{object}{The result obtained by \code{\link{tfbs.enrichmentTest}}.} 15 | \item{pv.threshold}{The p-value threshold for significant motifs.} 16 | \item{pv.adj}{P-values adjust method for \code{p.adjust} function. The available values are "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr" or "none".} 17 | \item{\dots}{Additional arguments affecting the summary produced.} 18 | } 19 | \details{ 20 | A data frame with 6 colums is returned. 21 | } 22 | \value{ 23 | The results is a data frame including 6 columns, 24 | \item{motif.id }{Motif ID} 25 | \item{tf.name }{TF Name} 26 | \item{Npos }{Read count in positive loci.} 27 | \item{expected }{Read count in negative loci.} 28 | \item{fe.ratio}{The ratio of read counts between positive loci and negative loci. } 29 | \item{starch}{Cpmporessed Bed filename} 30 | \item{pvalue}{p-value} 31 | \item{pv.adj}{adjusted p-value by multiple comparson method.} 32 | } 33 | \seealso{ 34 | See also as \code{\link{tfbs.enrichmentTest}}. 35 | } 36 | \keyword{summary} 37 | \keyword{Enrichment} 38 | -------------------------------------------------------------------------------- /rtfbsdb/man/summary.tfbs.finding.Rd: -------------------------------------------------------------------------------- 1 | \name{summary.tfbs.finding} 2 | \alias{summary.tfbs.finding} 3 | \title{ 4 | Summarize scanning results. 5 | } 6 | \description{ 7 | Return a data frame with summarized TF sites for every motif if the calling parameter is "matches". 8 | } 9 | \usage{ 10 | \method{summary}{tfbs.finding}(object, \dots) 11 | } 12 | \arguments{ 13 | \item{object}{The result obtained by \code{\link{tfbs.scanTFsite}}. } 14 | \item{\dots}{Additional arguments affecting the summary produced.} 15 | } 16 | \details{ 17 | \code{summary} in class of \code{tfbs.finding} is returned. 18 | } 19 | \value{ 20 | This function will return a data frame with summarized TF sites for every motif if the calling parameter is "matches", otherwise, NULL will be returned. 21 | } 22 | \seealso{ 23 | See Also as \code{\link{tfbs.scanTFsite}} 24 | } 25 | \keyword{ summary } 26 | \keyword{Scanning} 27 | -------------------------------------------------------------------------------- /rtfbsdb/man/tfbs.db.class.Rd: -------------------------------------------------------------------------------- 1 | \name{tfbs.db-class} 2 | \Rdversion{1.1} 3 | \docType{class} 4 | \alias{tfbs.db-class} 5 | 6 | \title{Class \code{"tfbs.db"}} 7 | \description{ 8 | Abstract class for motif dataset. The CisBP class is a son class of tfbs.db. 9 | } 10 | \section{Objects from the Class}{ 11 | Now code or function can be used to create this class. 12 | } 13 | \section{Slots}{ 14 | \describe{ 15 | \item{\code{species}:}{Species name. } 16 | } 17 | } 18 | \section{Methods}{ 19 | No methods defined with class "tfbs.db" in the signature. 20 | } 21 | 22 | \seealso{ 23 | \code{"\linkS4class{CisBP.db}"} inherits this class. 24 | 25 | } 26 | \examples{ 27 | showClass("tfbs.db") 28 | } 29 | \keyword{classes} 30 | -------------------------------------------------------------------------------- /rtfbsdb/man/tfbs.dirs.Rd: -------------------------------------------------------------------------------- 1 | \name{tfbs.dirs} 2 | \alias{tfbs.dirs} 3 | \title{ 4 | Create a tfbs object from the folders. 5 | } 6 | \description{ 7 | Create a tfbs object from all the PWM files found in the supplied folders. 8 | } 9 | \usage{ 10 | tfbs.dirs(..., 11 | species = "Homo_sapiens", 12 | args.read.motif = NULL, 13 | pattern = glob2rx("*.pwm"), 14 | recursive = FALSE) 15 | } 16 | \arguments{ 17 | \item{\dots}{ Multiple strings, one or more folders can be used in this function. } 18 | \item{species}{ String, including the species name.} 19 | \item{args.read.motif}{ List, including \emph{pseudocount}, \emph{force_even} or other parameters used in \code{read.table} function.} 20 | \item{pattern}{String, a character vector specifying regular expression and wlidcards. } 21 | \item{recursive}{Logical, indicating the loading recursively descends into subfolders or not, default: FALSE.} 22 | } 23 | \details{ 24 | 25 | Two parameters in the list of \code{args.read.motif} can be used:\cr 26 | pseudocount: log value for zero value in PWM matrix, default is -7.\cr 27 | force_even: whether the PWM matrix with odd size needs to be even.\cr 28 | 29 | } 30 | \value{ 31 | A tfbs object collecting all the PWM files in the specified folders. For the details of tfbs object, please see \code{\link{tfbs}} 32 | } 33 | \seealso{ 34 | The structure of tfbs object is described in \code{"\linkS4class{tfbs}"} 35 | } 36 | \examples{ 37 | 38 | fs.dir <- system.file("extdata","", package="rtfbsdb") 39 | tfs <- tfbs.dirs( fs.dir, 40 | args.read.motif = list(pseudocount=-7, header=TRUE, sep="\t" , row.names=1) ); 41 | str(tfs); 42 | 43 | } 44 | 45 | \keyword{tfbs object} 46 | -------------------------------------------------------------------------------- /rtfbsdb/man/tfbs.drawLogosForClusters.Rd: -------------------------------------------------------------------------------- 1 | \name{tfbs.drawLogosForClusters} 2 | \alias{tfbs.drawLogosForClusters} 3 | \title{ 4 | Draw the motif logos by clustering. 5 | } 6 | \description{ 7 | Draw the motif logos by one cluster per page. 8 | } 9 | \usage{ 10 | tfbs.drawLogosForClusters(tfbs, file.pdf, nrow.per.page=6, vertical=TRUE ) 11 | } 12 | \arguments{ 13 | \item{tfbs}{A tfbs object(\code{"\linkS4class{tfbs}"}).} 14 | \item{file.pdf }{ String indicating a PDF eilname.} 15 | \item{nrow.per.page }{ Number indicating row count in each page.} 16 | \item{vertical }{ Vertical composition or horizontal composition.} 17 | } 18 | \details{ 19 | It is different with \code{\link{tfbs.drawLogo}} which is capable of printing out motif logos in group. This group is calculated by the \code{\link{tfbs.clusterMotifs}}, not is classfied by any group filed. 20 | } 21 | \value{ 22 | No return value. 23 | } 24 | \seealso{ 25 | See Also as \code{\link{tfbs.clusterMotifs}} 26 | } 27 | \examples{ 28 | 29 | # Load the internal CisBP data set 30 | db <- CisBP.extdata("Homo_sapiens"); 31 | 32 | # Create a tfbs object by querying the meta file of CisBP dataset. 33 | tfs <- tfbs.createFromCisBP(db, motif_type="ChIP-seq", tf.information.type=1 ); 34 | 35 | # Cluster the motifs using the "cors" method 36 | tfs <- tfbs.clusterMotifs(tfs, method="apcluster", 37 | pdf.heatmap = "test-heatmap1.pdf" ); 38 | show(tfs@cluster); 39 | 40 | # draw motif logos on one group per page. 41 | tfbs.drawLogosForClusters(tfs, "test-cluster1.pdf") 42 | 43 | # draw motif logos on one group per page. 44 | tfbs.drawLogosForClusters(tfs, "test-cluster2.pdf", nrow.per.page=5 ) 45 | 46 | 47 | } 48 | \keyword{tfbs object} 49 | \keyword{Clustering} 50 | \keyword{Logo} 51 | -------------------------------------------------------------------------------- /rtfbsdb/man/tfbs.getDistanceMatrix.Rdxx: -------------------------------------------------------------------------------- 1 | \name{tfbs.getDistanceMatrix} 2 | \alias{tfbs.getDistanceMatrix} 3 | \title{ 4 | Calcuate a distance matrix with Pearson's R values. 5 | } 6 | \description{ 7 | Compare any two motifs and return a matrix with Pearson's R values. 8 | } 9 | \usage{ 10 | tfbs.getDistanceMatrix(tfbs, ncores = 3, BG = log(c(0.25, 0.25, 0.25, 0.25))) 11 | } 12 | \arguments{ 13 | \item{tfbs}{A tfbs object(\code{"\linkS4class{tfbs}"}).} 14 | \item{ncores}{Number, the number of cores to use simultaneously.} 15 | \item{BG}{The log value of probabilities for nucleotide A, C, G and T as Backgroud computing.} 16 | } 17 | \details{ 18 | Please do it parallel computation if you can use multi-cores because the calculation takes long time. 19 | } 20 | 21 | \value{ 22 | A tfbs object with new distance matrix (@distancematrix). 23 | } 24 | \seealso{ 25 | \code{"\linkS4class{tfbs}"} 26 | } 27 | \examples{ 28 | 29 | db <- CisBP.extdata("Homo_sapiens"); 30 | tfs <- tfbs.createFromCisBP(db, family_name="AP-2"); 31 | tfs0 <- tfbs.getDistanceMatrix(tfs, ncores=1); 32 | 33 | } 34 | \keyword{tfbs object} 35 | \keyword{Distance matrix} 36 | -------------------------------------------------------------------------------- /rtfbsdb/man/tfbs.reportEnrichment.Rd: -------------------------------------------------------------------------------- 1 | \name{tfbs.reportEnrichment} 2 | \alias{tfbs.reportEnrichment} 3 | \title{ 4 | Output report for enrichment results. 5 | } 6 | \description{ 7 | Output enrichment results to a PDF report which includes motif names, counts of TF site, p-value, enrichment ratio and motif logos. 8 | } 9 | \usage{ 10 | tfbs.reportEnrichment(tfbs, r.comp, 11 | file.pdf = NA, 12 | report.size = "letter", 13 | report.title = "", 14 | enrichment.type = c ("both", "enriched", "depleted"), 15 | sig.only = TRUE, 16 | pv.threshold = 0.05, 17 | pv.adj = NA, 18 | sorted = c ("pvalue", "enrich.ratio")) 19 | } 20 | \arguments{ 21 | \item{tfbs}{A tfbs object, see also \code{"\linkS4class{tfbs}"} } 22 | \item{r.comp}{A result object from the function of \code{\link{tfbs.enrichmentTest}}} 23 | \item{file.pdf}{String, the file name of PDF report.} 24 | \item{report.size}{String, the page size ( default="letter")} 25 | \item{report.title}{String, the report title. } 26 | \item{enrichment.type}{String, three values are available for significant motifs to be printed out.(default="both").} 27 | \item{sig.only}{String, indicating whether only significant motifs are outputted or not.(default=TRUE).} 28 | \item{pv.threshold}{Numeric value,indicating whether the different threshold of p-value is applied to select the significant motifs. } 29 | \item{pv.adj}{String,indicating whether the different correction metod of p-value is applied to select the significant motifs. } 30 | \item{sorted}{String,indicating which field is used to sort the results and print in the report. (default="pvalue") } 31 | } 32 | \details{ 33 | The table with 7 columns is outputted into a PDF report within letter size. \cr 34 | Two color bars are used to display p-values and enrichment ratios. Motif logos are shown visually in each row. 35 | } 36 | \value{ 37 | No return values. 38 | } 39 | \seealso{ 40 | \code{\link{tfbs.enrichmentTest}}, \code{\link{summary.tfbs.enrichment}}. 41 | } 42 | \examples{ 43 | # see examples in tfbs.enrichmentTest 44 | } 45 | 46 | \keyword{ tfbs object } 47 | \keyword{ Enrichment } 48 | -------------------------------------------------------------------------------- /rtfbsdb/man/tfbs.reportFinding.Rd: -------------------------------------------------------------------------------- 1 | \name{tfbs.reportFinding} 2 | \alias{tfbs.reportFinding} 3 | \title{ 4 | Make report for scanning results. 5 | } 6 | \description{ 7 | Output a PDF report includes motif names, counts of TF site and motif logos. 8 | } 9 | \usage{ 10 | tfbs.reportFinding(tfbs, 11 | r.scan, 12 | file.pdf = NA, 13 | report.size = "letter", 14 | report.title = "") 15 | } 16 | \arguments{ 17 | \item{tfbs}{A tfbs object, see also \code{"\linkS4class{tfbs}"} } 18 | \item{r.scan}{A result object from the function of \code{\link{tfbs.scanTFsite}}} 19 | \item{file.pdf}{String, the file name of PDF report.} 20 | \item{report.size}{String, the page size ( default="letter")} 21 | \item{report.title}{String, the report title. } 22 | 23 | } 24 | \details{ 25 | The table with 4 columns is outputted into a PDF report within letter size. \cr 26 | Motif logos are shown visually in each row. 27 | } 28 | \value{ 29 | No return values. 30 | } 31 | 32 | \seealso{ 33 | \code{\link{tfbs.scanTFsite}}, \code{\link{print.tfbs.finding}} 34 | } 35 | 36 | \examples{ 37 | #See example in tfbs.scanTFsite 38 | } 39 | \keyword{ tfbs object } 40 | \keyword{Scanning} 41 | -------------------------------------------------------------------------------- /rtfbsdb/man/tfbs.selectByGeneExp.Rd: -------------------------------------------------------------------------------- 1 | \name{tfbs.selectByGeneExp} 2 | \alias{tfbs.selectByGeneExp} 3 | \title{ 4 | Motif selection by gene expression level. 5 | } 6 | \description{ 7 | Select the motifs with minimum p-value from each group of clustering. 8 | } 9 | \usage{ 10 | tfbs.selectByGeneExp(tfbs) 11 | } 12 | \arguments{ 13 | \item{tfbs}{A tfbs object (\code{"\linkS4class{tfbs}"}) with the data frame of gene expression level.} 14 | } 15 | \details{ 16 | The function of \code{\link{tfbs.getExpression}} should be successfully called and the results of gene expression should be returned before this function is called. The indexes of selected motifs will be used in the function of \code{\link{tfbs.enrichmentTest}} or \code{\link{tfbs.scanTFsite}}. 17 | 18 | } 19 | \value{ 20 | New tfbs object with the selected indices is returned(tfbs@cluster). The 3rd column of tfbs@cluster is added or updated as the select flag(1:selected, 0:unselected). 21 | } 22 | \seealso{ 23 | See Also as \code{\link{tfbs.selectByRandom}}, \code{\link{tfbs.getExpression}} 24 | } 25 | \examples{ 26 | 27 | db <- CisBP.extdata("Homo_sapiens"); 28 | 29 | tfs <- tfbs.createFromCisBP(db, family_name="AP-2"); 30 | 31 | 32 | file.bigwig.minus <- system.file("extdata", 33 | "GSM1480327_K562_PROseq_chr19_minus.bw", package="rtfbsdb") 34 | file.bigwig.plus <- system.file("extdata", 35 | "GSM1480327_K562_PROseq_chr19_plus.bw", package="rtfbsdb") 36 | hg19.twobit <- system.file("extdata","hg19.chr19.2bit", package="rtfbsdb") 37 | gencode.gtf <- system.file("extdata", 38 | "gencode.v19.annotation.chr19.gtf.gz", package="rtfbsdb") 39 | 40 | tfs <- tfbs.getExpression(tfs, hg19.twobit, gencode.gtf, 41 | file.bigwig.plus, file.bigwig.minus, ncore=1); 42 | 43 | tfs <- tfbs.clusterMotifs(tfs, pdf.heatmap="test-AP2-heatmap.pdf" ); 44 | 45 | tfs <- tfbs.selectByGeneExp( tfs ); 46 | 47 | show(tfs@cluster); 48 | 49 | } 50 | \keyword{tfbs object} 51 | \keyword{Clustering} 52 | \keyword{Selection} 53 | -------------------------------------------------------------------------------- /rtfbsdb/man/tfbs.selectByRandom.Rd: -------------------------------------------------------------------------------- 1 | \name{tfbs.selectByRandom} 2 | \alias{tfbs.selectByRandom} 3 | \title{ 4 | Random motif selection 5 | } 6 | \description{ 7 | Select the motifs randomly from each group of clustering. 8 | } 9 | \usage{ 10 | tfbs.selectByRandom(tfbs) 11 | } 12 | \arguments{ 13 | \item{tfbs}{A tfbs object(\code{"\linkS4class{tfbs}"}).} 14 | } 15 | \details{ 16 | The indexes of selected motifs can be used in the function of \code{\link{tfbs.enrichmentTest}} or \code{\link{tfbs.scanTFsite}}. 17 | } 18 | \value{ 19 | New tfbs object with the selected indices is returned(tfbs@cluster). The 3rd column of tfbs@cluster is added or updated as the select flag(1:selected, 0:unselected). 20 | } 21 | \seealso{ 22 | See Also as \code{\link{tfbs.selectByGeneExp}}, \code{\link{tfbs.getExpression}} 23 | } 24 | \examples{ 25 | 26 | db <- CisBP.extdata("Homo_sapiens"); 27 | 28 | tfs <- tfbs.createFromCisBP(db, family_name="AP-2"); 29 | 30 | tfs <- tfbs.clusterMotifs(tfs, pdf.heatmap="test-AP2-heatmap.pdf" ); 31 | 32 | tfs <- tfbs.selectByRandom(tfs ); 33 | 34 | show(tfs@cluster); 35 | 36 | } 37 | \keyword{tfbs object} 38 | \keyword{Selection} 39 | \keyword{Clustering} 40 | 41 | -------------------------------------------------------------------------------- /test/cisbp.test.R: -------------------------------------------------------------------------------- 1 | # 2 | # Test a full procedure of CisBP.db class 3 | # 4 | 5 | library(rtfbsdb) 6 | 7 | #downloa human databse 8 | db1 <- CisBP.download("Homo_sapiens"); 9 | 10 | #downloa mouse databse 11 | db2 <- CisBP.download("Mus_musculus"); 12 | 13 | #reading data from zip file 14 | db3 <- CisBP.zipload(db2@zip.file, species="Mus_musculus"); 15 | 16 | #reading data from inner file 17 | db4 <- CisBP.extdata(species="Homo_sapiens"); 18 | 19 | df <- CisBP.getTFinformation( db1, tf.information.type=2 ); 20 | 21 | show(head(df)); 22 | 23 | #group method 24 | 25 | gr1 <-CisBP.group(db1, group.by="family_name", tf.information.type=1 ); 26 | 27 | gr2 <-CisBP.group(db2, group.by="tf_status", tf.information.type=1 ); 28 | 29 | gr3 <-CisBP.group(db3, group.by="tf_status", tf.information.type=2); 30 | 31 | gr4 <-CisBP.group(db4, group.by="tf_status", tf.information.type=3); 32 | 33 | gr5 <-CisBP.group(db3, group.by="motif_type", tf.information.type=3); 34 | 35 | gr6 <-CisBP.group(db3, group.by="msource_id", tf.information.type=3); 36 | 37 | df1 <- CisBP.getTFinformation(db3); 38 | 39 | df2 <- CisBP.getTFinformation(db3, tf.information.type=2); 40 | 41 | #find method 42 | tfs0 <-tfbs.createFromCisBP(db4, family_name="Homeodomain", tf_status="D", motif_type="ChIP-seq", msource_id= "MS01_1.01", tf.information.type=1 ); 43 | 44 | tfs1 <-tfbs.createFromCisBP(db4, family_name="Homeodomain", tf_status="D" ); 45 | 46 | tfs2 <-tfbs.createFromCisBP(db4, motif_type="ChIP-seq" ); 47 | 48 | tfs3 <-tfbs.createFromCisBP(db4, tf.information.type=2 ); 49 | 50 | save.image(file="cisbp.test.rdata"); -------------------------------------------------------------------------------- /test/dog.export.R: -------------------------------------------------------------------------------- 1 | library(rtfbsdb) 2 | 3 | file.twoBit_path <- "canFam3.2bit"; 4 | 5 | db <- CisBP.zipload("Canis_familiaris_2018_12_01_11_26_pm.zip", "canFam3"); 6 | tfs <- tfbs.createFromCisBP(db); 7 | df <- as.data.frame(table(tfs@tf_info$Motif_Type)) 8 | df <- df[df[,2]!=0,] 9 | 10 | tf_info <- tfs@tf_info[, c("Motif_ID", "TF_Name")]; 11 | tf_info <- do.call("rbind", lapply(unique(tf_info$Motif_ID), function(x){ 12 | idx <- which( as.character(tf_info$Motif_ID) == as.character(x) ); 13 | if(NROW(idx)>4) 14 | return(data.frame(Motif_ID=x, TF_Name=paste(c(as.character(tf_info[idx, "TF_Name"])[1:4], "..."), collapse=","))) 15 | else if( NROW(idx)>1 ) 16 | return(data.frame(Motif_ID=x, TF_Name=paste(as.character(tf_info[idx, "TF_Name"]), collapse=","))) 17 | else 18 | return(data.frame(Motif_ID=x, TF_Name=as.character(tf_info[idx, "TF_Name"]))) 19 | })); 20 | 21 | write.table(tf_info, file="canFam3.tf.info", quote=F, row.names=F, col.names=F, sep="\t"); 22 | 23 | for (Motif_Type in df$Var1) 24 | { 25 | if (!file.exists(paste0("Motif_Type_", Motif_Type, ".rdata"))) 26 | { 27 | tfs1 <- tfbs.createFromCisBP(db, motif_type=Motif_Type); 28 | dScan <- tfbs.scanTFsite( tfs1, file.twoBit_path, ncores=20); 29 | save(dScan, file=paste0("Motif_Type_", Motif_Type, ".rdata") ); 30 | rm(dScan); 31 | gc(); 32 | } 33 | } 34 | 35 | make_bed<-function( df_bed, out_file) 36 | { 37 | options(scipen=99, digits=4); 38 | file.tmp <- tempfile(fileext=".bed"); 39 | write.table( df_bed, file=file.tmp, row.names=FALSE, col.names=FALSE, quote=FALSE, sep="\t"); 40 | system(paste( "sort-bed ", file.tmp, " | bgzip -f > ", out_file, ".gz", sep="") ); 41 | unlink(file.tmp) 42 | } 43 | 44 | 45 | for (Motif_Type in df$Var1) 46 | { 47 | if (file.exists(paste0("Motif_Type_", Motif_Type, ".rdata"))) 48 | { 49 | load( paste0("Motif_Type_", Motif_Type, ".rdata") ) ; 50 | 51 | for (i in 1:NROW(dScan$summary)) 52 | { 53 | dScan.bed <- dScan$result[[i]]; 54 | out_file <- paste0("temp/", as.character(dScan$summary$Motif_ID[i]), ".bed"); 55 | if(!file.exists(paste0(out_file, ".gz") ) ) 56 | make_bed( dScan.bed, out_file); 57 | } 58 | } 59 | } 60 | 61 | 62 | -------------------------------------------------------------------------------- /test/hg19.exportTF.R: -------------------------------------------------------------------------------- 1 | library(rtfbsdb) 2 | 3 | 4 | file.dREG.all.bed <- "/home/zw355/src/rtfbs_db/test/G1.dREG.peak.score.bed.gz" 5 | file.twoBit_path <- "/local/storage/data/hg19/hg19.2bit"; 6 | 7 | 8 | db <- CisBP.extdata("Homo_sapiens"); 9 | tfs <- tfbs.createFromCisBP(db); 10 | df <- as.data.frame(table(tfs@tf_info$Motif_Type)) 11 | df <- df[df[,2]!=0,] 12 | 13 | tf_info <- tfs@tf_info[, c("Motif_ID", "TF_Name")]; 14 | tf_info <- do.call("rbind", lapply(unique(tf_info$Motif_ID), function(x){ 15 | idx <- which( as.character(tf_info$Motif_ID) == as.character(x) ); 16 | if(NROW(idx)>4) 17 | return(data.frame(Motif_ID=x, TF_Name=paste(c(as.character(tf_info[idx, "TF_Name"])[1:4], "..."), collapse=","))) 18 | else if( NROW(idx)>1 ) 19 | return(data.frame(Motif_ID=x, TF_Name=paste(as.character(tf_info[idx, "TF_Name"]), collapse=","))) 20 | else 21 | return(data.frame(Motif_ID=x, TF_Name=as.character(tf_info[idx, "TF_Name"]))) 22 | })); 23 | 24 | write.table(tf_info, file="hg19.tf.info", quote=F, row.names=F, col.names=F, sep="\t"); 25 | 26 | for (Motif_Type in df$Var1) 27 | { 28 | if (!file.exists(paste0("hg19_Motif_Type_", Motif_Type, ".rdata"))) 29 | { 30 | tfs1 <- tfbs.createFromCisBP(db, motif_type=Motif_Type); 31 | dScan <- tfbs.scanTFsite( tfs1, file.twoBit_path, ncores=5); 32 | save(dScan, file=paste0("hg19_Motif_Type_", Motif_Type, ".rdata") ); 33 | rm(dScan); 34 | gc(); 35 | } 36 | } 37 | 38 | for (Motif_Type in df$Var1) 39 | { 40 | if (file.exists(paste0("hg19_Motif_Type_", Motif_Type, ".rdata"))) 41 | { 42 | load( paste0("hg19_Motif_Type_", Motif_Type, ".rdata") ) ; 43 | 44 | for (i in 1:NROW(dScan$summary)) 45 | { 46 | dScan.bed <- dScan$result[[i]]; 47 | out_file <- paste0("temp/", as.character(dScan$summary$Motif_ID[i]), ".bed"); 48 | if(!file.exists(paste0(out_file, ".gz") ) ) 49 | make_bed( dScan.bed, out_file); 50 | } 51 | } 52 | } -------------------------------------------------------------------------------- /test/horse.export.R: -------------------------------------------------------------------------------- 1 | library(rtfbsdb) 2 | 3 | file.twoBit_path <- "equCab2.2bit"; 4 | 5 | db <- CisBP.zipload("Equus_caballus_2018_12_01_11:38_pm.zip", "horse"); 6 | tfs <- tfbs.createFromCisBP(db); 7 | df <- as.data.frame(table(tfs@tf_info$Motif_Type)) 8 | df <- df[df[,2]!=0,] 9 | 10 | tf_info <- tfs@tf_info[, c("Motif_ID", "TF_Name")]; 11 | tf_info <- do.call("rbind", lapply(unique(tf_info$Motif_ID), function(x){ 12 | idx <- which( as.character(tf_info$Motif_ID) == as.character(x) ); 13 | if(NROW(idx)>4) 14 | return(data.frame(Motif_ID=x, TF_Name=paste(c(as.character(tf_info[idx, "TF_Name"])[1:4], "..."), collapse=","))) 15 | else if( NROW(idx)>1 ) 16 | return(data.frame(Motif_ID=x, TF_Name=paste(as.character(tf_info[idx, "TF_Name"]), collapse=","))) 17 | else 18 | return(data.frame(Motif_ID=x, TF_Name=as.character(tf_info[idx, "TF_Name"]))) 19 | })); 20 | 21 | write.table(tf_info, file="equCab2.tf.info", quote=F, row.names=F, col.names=F, sep="\t"); 22 | 23 | for (Motif_Type in df$Var1) 24 | { 25 | if (!file.exists(paste0("Motif_Type_", Motif_Type, ".rdata"))) 26 | { 27 | tfs1 <- tfbs.createFromCisBP(db, motif_type=Motif_Type); 28 | dScan <- tfbs.scanTFsite( tfs1, file.twoBit_path, ncores=20); 29 | save(dScan, file=paste0("Motif_Type_", Motif_Type, ".rdata") ); 30 | rm(dScan); 31 | gc(); 32 | } 33 | } 34 | 35 | make_bed<-function( df_bed, out_file) 36 | { 37 | options(scipen=99, digits=4); 38 | file.tmp <- tempfile(fileext=".bed"); 39 | write.table( df_bed, file=file.tmp, row.names=FALSE, col.names=FALSE, quote=FALSE, sep="\t"); 40 | system(paste( "sort-bed ", file.tmp, " | bgzip -f > ", out_file, ".gz", sep="") ); 41 | unlink(file.tmp) 42 | } 43 | 44 | 45 | for (Motif_Type in df$Var1) 46 | { 47 | if (file.exists(paste0("Motif_Type_", Motif_Type, ".rdata"))) 48 | { 49 | load( paste0("Motif_Type_", Motif_Type, ".rdata") ) ; 50 | 51 | for (i in 1:NROW(dScan$summary)) 52 | { 53 | dScan.bed <- dScan$result[[i]]; 54 | out_file <- paste0("temp/", as.character(dScan$summary$Motif_ID[i]), ".bed"); 55 | if(!file.exists(paste0(out_file, ".gz") ) ) 56 | make_bed( dScan.bed, out_file); 57 | } 58 | } 59 | } 60 | 61 | 62 | -------------------------------------------------------------------------------- /test/mm10.export.R: -------------------------------------------------------------------------------- 1 | library(rtfbsdb) 2 | 3 | file.twoBit_path <- "/local/storage/data/mm10/mm10.2bit"; 4 | 5 | db <- CisBP.extdata("Mus_musculus"); 6 | tfs <- tfbs.createFromCisBP(db); 7 | df <- as.data.frame(table(tfs@tf_info$Motif_Type)) 8 | df <- df[df[,2]!=0,] 9 | 10 | tf_info <- tfs@tf_info[, c("Motif_ID", "TF_Name")]; 11 | tf_info <- do.call("rbind", lapply(unique(tf_info$Motif_ID), function(x){ 12 | idx <- which( as.character(tf_info$Motif_ID) == as.character(x) ); 13 | if(NROW(idx)>4) 14 | return(data.frame(Motif_ID=x, TF_Name=paste(c(as.character(tf_info[idx, "TF_Name"])[1:4], "..."), collapse=","))) 15 | else if( NROW(idx)>1 ) 16 | return(data.frame(Motif_ID=x, TF_Name=paste(as.character(tf_info[idx, "TF_Name"]), collapse=","))) 17 | else 18 | return(data.frame(Motif_ID=x, TF_Name=as.character(tf_info[idx, "TF_Name"]))) 19 | })); 20 | 21 | write.table(tf_info, file="mm10.tf.info", quote=F, row.names=F, col.names=F, sep="\t"); 22 | 23 | 24 | for (Motif_Type in df$Var1) 25 | { 26 | if (!file.exists(paste0("Motif_Type_", Motif_Type, ".rdata"))) 27 | { 28 | cat("Motif_Type=", Motif_Type, "\n"); 29 | tfs1 <- tfbs.createFromCisBP(db, motif_type=Motif_Type); 30 | dScan <- tfbs.scanTFsite( tfs1, file.twoBit_path, ncores=20); 31 | save(dScan, file=paste0("Motif_Type_", Motif_Type, ".rdata") ); 32 | rm(dScan); 33 | gc(); 34 | } 35 | } 36 | 37 | make_bed<-function( df_bed, out_file) 38 | { 39 | options(scipen=99, digits=4); 40 | file.tmp <- tempfile(fileext=".bed"); 41 | write.table( df_bed, file=file.tmp, row.names=FALSE, col.names=FALSE, quote=FALSE, sep="\t"); 42 | system(paste( "sort-bed ", file.tmp, " | bgzip -f > ", out_file, ".gz", sep="") ); 43 | unlink(file.tmp) 44 | } 45 | 46 | 47 | for (Motif_Type in df$Var1) 48 | { 49 | if (file.exists(paste0("Motif_Type_", Motif_Type, ".rdata"))) 50 | { 51 | cat("load =", Motif_Type, "\n"); 52 | load( paste0("Motif_Type_", Motif_Type, ".rdata") ) ; 53 | 54 | for (i in 1:NROW(dScan$summary)) 55 | { 56 | dScan.bed <- dScan$result[[i]]; 57 | out_file <- paste0("temp/", as.character(dScan$summary$Motif_ID[i]), ".bed"); 58 | if(!file.exists(paste0(out_file, ".gz") ) ) 59 | make_bed( dScan.bed, out_file); 60 | } 61 | } 62 | } 63 | 64 | 65 | -------------------------------------------------------------------------------- /test/motif_intersected_sorted_uniq_sortedByAbsLogRatio.rdata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Danko-Lab/rtfbs_db/a29f73b24e8984aad8bcd1227b06446ebef44b08/test/motif_intersected_sorted_uniq_sortedByAbsLogRatio.rdata -------------------------------------------------------------------------------- /test/rtfbs.plotEnrichment.test.R: -------------------------------------------------------------------------------- 1 | load("motif_intersected_sorted_uniq_sortedByAbsLogRatio.rdata") 2 | 3 | library(rtfbsdb); 4 | 5 | #db <- CisBP.extdata("Homo_sapiens"); 6 | #tfs <- tfbs.createFromCisBP(db); 7 | 8 | load("tfs.rdata"); 9 | 10 | tfbs.plotEnrichment(tfs, t.comp, file.pdf="enrich-qqplot2.pdf", plot.type="nonpolar", enrichment.type="both", options=list( width=4, zoom.motif.label=1.5, zoom.motif.logo=2, zoom.tick=1, zoom.label=1, zoom.legend.label=1 )) 11 | 12 | tfbs.plotEnrichment(tfs, t.comp, file.pdf="enrich-qqplot1.pdf", plot.type="nonpolar", enrichment.type="enriched") 13 | 14 | tfbs.plotEnrichment(tfs, t.comp, file.pdf="enrich-qqplot3.pdf", plot.type="polar", enrichment.type="depleted") 15 | 16 | tfbs.plotEnrichment(tfs, t.comp, file.pdf="enrich-qqplot4.pdf", plot.type="polar", enrichment.type="both") 17 | 18 | -------------------------------------------------------------------------------- /test/tfbs.G1.scan.R: -------------------------------------------------------------------------------- 1 | # 2 | # Test a tfbs.scanTSsite procedure of tfbs class 3 | # 4 | 5 | library(rtfbsdb) 6 | 7 | detach("package:rtfbsdb", unload=TRUE); 8 | 9 | library(rtfbsdb) 10 | 11 | 12 | file.dREG.all.bed <- "/workdir/zw355/proj/prj10-dreg/new-rf-201803/G1/G1.dREG.peak.score.bed.gz" 13 | file.twoBit_path <- "/fs/cbsudanko/storage/data/hg19/hg19.2bit" 14 | 15 | db <- CisBP.extdata("Homo_sapiens"); 16 | tfs <- tfbs.createFromCisBP(db); 17 | 18 | dREG_bed <- read.table(file.dREG.all.bed, header=F); 19 | dREG_bed <- dREG_bed[ dREG_bed[,1]=="chr1", ] 20 | 21 | dScan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_bed, return.type="writedb", file.prefix="todo-rm", ncores=12); 22 | 23 | dScan 24 | 25 | dScan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_bed, ncores=12); 26 | 27 | save(dScan, file="G1.dREG.peak.rdata"); 28 | 29 | for (i in 1:NROW(dScan$result)) write.table(dScan$result[[i]], file=paste("dREG-", dScan$summary[i,2], "-", dScan$summary[i,1], ".bed", sep=""), quote=F, row.names=F, col.names=F, sep="\t"); 30 | -------------------------------------------------------------------------------- /test/tfbs.comp.bat: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #---------------------------------------------------- 4 | # Generic SLURM script 5 | #---------------------------------------------------- 6 | 7 | #SBATCH -J tfbs.class.test # Job name 8 | #SBATCH -o myjob.%j.out # stdout; %j expands to jobid 9 | #SBATCH -e myjob.%j.err # stderr; skip to combine stdout and stderr 10 | #SBATCH -p normal # queue 11 | #SBATCH -N 1 -n 1 # one node and one task 12 | #SBATCH -t 48:00:00 # max time 13 | #SBATCH --mail-user=zw355@cornell.edu 14 | #SBATCH --mail-type=ALL 15 | 16 | module load bedtools 17 | 18 | $R --vanilla --no-save < tfbs.comp.R > tfbs.comp.out 19 | 20 | 21 | -------------------------------------------------------------------------------- /test/tfbs.comp.full.R: -------------------------------------------------------------------------------- 1 | library(rtfbsdb) 2 | 3 | file.dREG.H.change.bed <- "/home/zw355/src/rtfbs_db/testdata/dREG.H.change.bed" 4 | file.dREG.all.bed <- "/home/zw355/src/rtfbs_db/testdata/dREG.all.bed" 5 | file.twoBit_path <- "/local/storage/data/hg19/hg19.2bit"; 6 | 7 | db <- CisBP.extdata("Homo_sapiens"); 8 | tfs <- tfbs.createFromCisBP(db); 9 | 10 | dREG_H_change_bed <- read.table(file.dREG.H.change.bed, header=F); 11 | dREG_all_bed <- read.table(file.dREG.all.bed, header=F); 12 | 13 | t <- tfbs.enrichmentTest( tfs, 14 | file.twoBit_path, 15 | dREG_H_change_bed, 16 | dREG_all_bed, 17 | gc.correction=TRUE, 18 | ncores = 21); 19 | 20 | tfbs.reportEnrichment(tfs, t, file.pdf="tfbs.comp.full.pdf", sig.only=F, report.title="TEST FULL"); 21 | 22 | save.image(file="tfbs.comp.full.rdata"); 23 | -------------------------------------------------------------------------------- /test/tfbs.dirs.test.R: -------------------------------------------------------------------------------- 1 | library(rtfbsdb) 2 | fs.dir <- system.file("extdata","", package="rtfbsdb") 3 | tfs <- tfbs.dirs( fs.dir, args.read.motif = list(pseudocount=-7, header=TRUE, sep="\t" , row.names=1) ); 4 | 5 | tfbs.drawLogo(tfsN, file.pdf="/home/zw355/temp/a/a.pdf"); 6 | 7 | file.twoBit <- "/home/zw355/src/rtfbs_db/testdata/hg19.2bit" 8 | gen.bed <- data.frame(chr="chr19", start=round(runif(10,1000000, 2000000)),stop=0, name="", score=0, strand="."); 9 | gen.bed$stop <- gen.bed$start + 3000; 10 | t1 <- tfbs.scanTFsite( tfs, file.twoBit, gen.bed=NULL, file.prefix="test.db", ncores = 1); 11 | 12 | 13 | library(rtfbsdb) 14 | db <- CisBP.extdata("Mus_musculus") 15 | tfRORb <- tfbs.createFromCisBP(db,tf_name = "Rorb",motif_id = NULL,msource_id = NULL,tf.information.type = 1) 16 | 17 | 18 | library(rtfbsdb) 19 | fs.dir <- "/home/zw355/temp" 20 | tfsN <- tfbs.dirs(fs.dir, species = "Mus_musculus", args.read.motif = list(header=TRUE, sep="\t", force_even=TRUE, row.names=1), pattern = glob2rx("*.pwm")) 21 | 22 | tfsN; 23 | 24 | tfbs.drawLogo(tfsN, file.pdf="/home/zw355/temp/a/a.pdf"); 25 | 26 | file.twoBit <- "/home/zw355/src/rtfbs_db/testdata/hg19.2bit" 27 | gen.bed <- data.frame(chr="chr19", start=round(runif(10,1000000, 2000000)),stop=0, name="", score=0, strand="."); 28 | gen.bed$stop <- gen.bed$start + 3000; 29 | t1 <- tfbs.scanTFsite( tfsN, file.twoBit, gen.bed=NULL, file.prefix="test.db", ncores = 1); 30 | 31 | 32 | 33 | tfsN <- tfbs.dirs(fs.dir, species = "Mus_musculus", args.read.motif = list(header=TRUE, sep="\t", force_even=TRUE), pattern = glob2rx("*.pwm")) 34 | tfsN; 35 | tfsN <- tfbs.dirs(fs.dir, species = "Mus_musculus", args.read.motif = list(header=TRUE, sep="\t", row.names=1), pattern = glob2rx("*.pwm")) 36 | tfsN; 37 | tfsN <- tfbs.dirs(fs.dir, species = "Mus_musculus", args.read.motif = list(header=TRUE, sep="\t"), pattern = glob2rx("*.pwm")) 38 | tfsN; 39 | 40 | 41 | -------------------------------------------------------------------------------- /test/tfbs.drawLogo.R: -------------------------------------------------------------------------------- 1 | detach("package:rtfbsdb", unload=TRUE); 2 | 3 | library(rtfbsdb) 4 | 5 | db <- CisBP.extdata("Homo_sapiens"); 6 | tfs <- tfbs.createFromCisBP( db ); 7 | 8 | motif_id <- c( "M5604_1.01", "M6001_1.01" , "M5440_1.01", "M5441_1.01", "M5162_1.01", "M5352_1.01"); 9 | tf_id <- c( "T093250_1.01", "T093251_1.01","T093252_1.01","T093253_1.01"); 10 | family_name<- c( "p53", "Homeodomain", "Paired box", "Pipsqueak"); 11 | 12 | 13 | #tfbs.drawLogo(tfbs, file.pdf, index=NA, tf_id=NA, motif_id=NA, tf_name=NA, family_name=NA, tf_status=NA, groupby=NA) 14 | 15 | tfbs.drawLogo(tfs, file.pdf="tfbs.drawLogo1.pdf", index=c(1:100), groupby="Family_Name"); 16 | 17 | tfbs.drawLogo(tfs, file.pdf="tfbs.drawLogo2.pdf", motif_id=motif_id, tf_id=tf_id, tf_name="AP-2", family_name=family_name, groupby="TF_Status"); 18 | 19 | tfbs.drawLogo(tfs, file.pdf="tfbs.drawLogo3.pdf", tf_status="D", groupby="TF_Status"); 20 | 21 | tfbs.drawLogo(tfs, file.pdf="tfbs.drawLogo4.pdf", index=c(1:100), groupby="TF_Status"); 22 | 23 | tfbs.drawLogo(tfs, file.pdf="tfbs.drawLogo5.pdf", groupby="TF_Status" ); 24 | -------------------------------------------------------------------------------- /test/tfbs.scan.R: -------------------------------------------------------------------------------- 1 | # 2 | # Test a tfbs.scanTSsite procedure of tfbs class 3 | # 4 | 5 | library(rtfbsdb) 6 | 7 | detach("package:rtfbsdb", unload=TRUE); 8 | 9 | library(rtfbsdb) 10 | 11 | 12 | file.dREG.H.change.bed <- "/home/zw355/src/rtfbs_db/testdata/dREG.H.change.bed" 13 | file.dREG.all.bed <- "/home/zw355/src/rtfbs_db/testdata/dREG.all.bed" 14 | file.twoBit_path <- "/local/storage/data/hg19/hg19.2bit"; 15 | 16 | 17 | db <- CisBP.extdata("Homo_sapiens"); 18 | tfs <- tfbs.createFromCisBP(db, family_name="AP-2"); 19 | 20 | dREG_H_change_bed <- read.table(file.dREG.H.change.bed, header=F); 21 | 22 | 23 | t1.scan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_H_change_bed, ncores=3); 24 | 25 | t2.scan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_H_change_bed, return.type="writedb", ncores=3); 26 | 27 | t3.scan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_H_change_bed, return.type="posteriors", ncores=1, threshold=8); 28 | 29 | t4.scan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_H_change_bed, return.type="maxposterior", ncores=1, threshold=8); 30 | 31 | t5.scan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_H_change_bed, ncores=3, file.prefix = "test.tfscan", threshold=0.05, threshold.type="fdr" ); 32 | 33 | t6.scan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_H_change_bed, ncores=3, file.prefix = "test.tfscan", threshold=0.05, threshold.type="fdr", gc.groups=5, background.order = 3 ); 34 | 35 | t7.scan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_H_change_bed, ncores=3, threshold=8, gc.groups=4, background.order = 3 ); 36 | 37 | t8.scan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_H_change_bed, ncores=3, return.type="writedb", file.prefix = "test.tfscan", threshold=0.05, threshold.type="fdr", gc.groups=5, background.order = 3 ); 38 | 39 | t9.scan <- tfbs.scanTFsite( tfs, file.twoBit_path, dREG_H_change_bed, ncores=3, return.type="matches", file.prefix = "test.tfscan", threshold=0.05, threshold.type="fdr", gc.groups=5, background.order = 3 ); 40 | 41 | 42 | t1.scan; 43 | 44 | t2.scan; 45 | 46 | t3.scan; 47 | 48 | t4.scan; 49 | 50 | t5.scan; 51 | 52 | t6.scan; 53 | 54 | t7.scan; 55 | 56 | t8.scan; 57 | 58 | t9.scan; 59 | 60 | tfbs.reportFinding(tfs, t9.scan, file.pdf="test-tfscan.pdf", report.title="AP-2 Results"); 61 | 62 | -------------------------------------------------------------------------------- /test/tfbs.scan.bat: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #---------------------------------------------------- 4 | # Generic SLURM script 5 | #---------------------------------------------------- 6 | 7 | #SBATCH -J tfbs.class.test # Job name 8 | #SBATCH -o myjob.%j.out # stdout; %j expands to jobid 9 | #SBATCH -e myjob.%j.err # stderr; skip to combine stdout and stderr 10 | #SBATCH -p normal # queue 11 | #SBATCH -N 1 -n 1 # one node and one task 12 | #SBATCH -t 48:00:00 # max time 13 | #SBATCH --mail-user=zw355@cornell.edu 14 | #SBATCH --mail-type=ALL 15 | 16 | module load bedtools 17 | 18 | $R --vanilla --no-save < tfbs.scan.R > tfbs.scan.out 19 | 20 | 21 | -------------------------------------------------------------------------------- /test/tfbs.test.R: -------------------------------------------------------------------------------- 1 | # 2 | # Test a full procedure of tfbs class 3 | # 4 | 5 | file.bigwig.plus <- "/home/zw355/src/rtfbs_db/testdata/GSM1480327_K562_PROseq_plus.bw"; 6 | file.bigwig.minus <- "/home/zw355/src/rtfbs_db/testdata/GSM1480327_K562_PROseq_minus.bw"; 7 | file.hg19 <- "/local/storage/data/hg19/hg19.2bit"; 8 | file.gencode.v19 <- "/local/storage/data/gencode/gencode.v19.annotation.gtf"; 9 | 10 | library(rtfbsdb) 11 | 12 | db <- CisBP.extdata("Homo_sapiens"); 13 | db.sum <- CisBP.group( db, group.by="family_name", tf.information.type=1); 14 | tfs <- tfbs.createFromCisBP( db ); 15 | 16 | tfs <- tfbs.getExpression( tfs, file.hg19, file.gencode.v19, file.bigwig.plus, file.bigwig.minus ); 17 | 18 | cluster.mat <- tfbs.clusterMotifs(tfs, pdf.heatmap="test-correlationMatrix.pdf") 19 | 20 | tfbs.drawLogo( tfs ,1 ) 21 | 22 | usemotifs1 <- tfbs.selectByRandom(tfs, cluster.mat); 23 | 24 | usemotifs2 <- tfbs.selectByGeneExp( tfs, cluster.mat ); 25 | 26 | save.image(file="test.tfbs.rdata"); 27 | 28 | q("no") 29 | -------------------------------------------------------------------------------- /test/tfbs.test.bat: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #---------------------------------------------------- 4 | # Generic SLURM script 5 | #---------------------------------------------------- 6 | 7 | #SBATCH -J tfbs.class.test # Job name 8 | #SBATCH -o myjob.%j.out # stdout; %j expands to jobid 9 | #SBATCH -e myjob.%j.err # stderr; skip to combine stdout and stderr 10 | #SBATCH -p normal # queue 11 | #SBATCH -N 1 -n 1 # one node and one task 12 | #SBATCH -t 48:00:00 # max time 13 | #SBATCH --mail-user=zw355@cornell.edu 14 | #SBATCH --mail-type=ALL 15 | 16 | module load bedtools 17 | 18 | $R --vanilla --no-save < tfbs.test.R > tfbs.test.out 19 | 20 | 21 | --------------------------------------------------------------------------------