├── LICENSE ├── Makefile ├── README.md ├── bin └── .gitignore ├── include ├── cram │ ├── cram.h │ ├── cram_codecs.h │ ├── cram_decode.h │ ├── cram_encode.h │ ├── cram_index.h │ ├── cram_io.h │ ├── cram_samtools.h │ ├── cram_stats.h │ ├── cram_structs.h │ ├── mFILE.h │ ├── md5.h │ ├── misc.h │ ├── open_trace_file.h │ ├── os.h │ ├── pooled_alloc.h │ ├── rANS_byte.h │ ├── rANS_static.h │ ├── sam_header.h │ ├── string_alloc.h │ ├── thread_pool.h │ ├── vlen.h │ └── zfio.h ├── htslib │ ├── bgzf.h │ ├── faidx.h │ ├── hfile.h │ ├── hfile_internal.h │ ├── hts.h │ ├── hts_defs.h │ ├── kfunc.h │ ├── khash.h │ ├── khash_str2int.h │ ├── klist.h │ ├── knetfile.h │ ├── kseq.h │ ├── ksort.h │ ├── kstring.h │ ├── regidx.h │ ├── sam.h │ ├── synced_bcf_reader.h │ ├── tbx.h │ ├── vcf.h │ ├── vcf_sweep.h │ ├── vcfutils.h │ └── version.h ├── samtools │ ├── bam.h │ ├── bam2bcf.h │ ├── bam_endian.h │ ├── bam_lpileup.h │ ├── bam_plbuf.h │ ├── bam_tview.h │ ├── errmod.h │ ├── kprobaln.h │ ├── sam.h │ ├── sam_header.h │ ├── sample.h │ ├── samtools.h │ ├── stats_isize.h │ └── version.h └── seqcode │ └── seqcode.h ├── objects ├── .gitignore ├── cram │ └── .gitignore ├── htslib │ └── .gitignore ├── samtools │ └── .gitignore └── seqcode │ └── .gitignore ├── src ├── cram │ ├── cram_codecs.c │ ├── cram_decode.c │ ├── cram_encode.c │ ├── cram_index.c │ ├── cram_io.c │ ├── cram_samtools.c │ ├── cram_stats.c │ ├── files.c │ ├── mFILE.c │ ├── md5.c │ ├── open_trace_file.c │ ├── pooled_alloc.c │ ├── rANS_static.c │ ├── sam_header.c │ ├── string_alloc.c │ ├── thread_pool.c │ ├── vlen.c │ └── zfio.c ├── htslib │ ├── bgzf.c │ ├── bgzip.c │ ├── faidx.c │ ├── hfile.c │ ├── hfile_irods.c │ ├── hfile_net.c │ ├── hts.c │ ├── htsfile.c │ ├── kfunc.c │ ├── knetfile.c │ ├── kstring.c │ ├── regidx.c │ ├── sam.c │ ├── synced_bcf_reader.c │ ├── tabix.c │ ├── tbx.c │ ├── vcf.c │ ├── vcf_sweep.c │ └── vcfutils.c ├── samtools │ ├── bam.c │ ├── bam2bcf.c │ ├── bam2bcf_indel.c │ ├── bam2depth.c │ ├── bam_aux.c │ ├── bam_cat.c │ ├── bam_color.c │ ├── bam_flags.c │ ├── bam_import.c │ ├── bam_index.c │ ├── bam_lpileup.c │ ├── bam_mate.c │ ├── bam_md.c │ ├── bam_plbuf.c │ ├── bam_plcmd.c │ ├── bam_reheader.c │ ├── bam_rmdup.c │ ├── bam_rmdupse.c │ ├── bam_sort.c │ ├── bam_split.c │ ├── bam_stat.c │ ├── bam_tview.c │ ├── bam_tview_curses.c │ ├── bam_tview_html.c │ ├── bamshuf.c │ ├── bamtk.c │ ├── bedcov.c │ ├── bedidx.c │ ├── cut_target.c │ ├── errmod.c │ ├── faidx.c │ ├── kprobaln.c │ ├── padding.c │ ├── phase.c │ ├── sam.c │ ├── sam_header.c │ ├── sam_view.c │ ├── sample.c │ ├── stats.c │ └── stats_isize.c └── seqcode │ ├── ColorManager.c │ ├── CombineGenomes.c │ ├── CombineTargetGenes.c │ ├── CombineTargetGenesMaps.c │ ├── Dictionary.c │ ├── GetFileSize.c │ ├── Output.c │ ├── OutputH.c │ ├── OutputR.c │ ├── ProcessBG.c │ ├── ProcessGenesMax.c │ ├── ProcessGenome.c │ ├── ProcessGenomePeaks.c │ ├── ProcessPeaks.c │ ├── ProcessPeaksLists.c │ ├── ProcessPeaksMarks.c │ ├── ProcessTargetGenes.c │ ├── ProcessTargetGenesGENE.c │ ├── ProcessTargetGenesGENEMaps.c │ ├── ProcessTargetGenesMaps.c │ ├── ProcessTargetGenesTES.c │ ├── ProcessTargetGenesTESMaps.c │ ├── ReadBGFile.c │ ├── ReadChrFile.c │ ├── ReadPeaksFile.c │ ├── ReadPhastConsFiles.c │ ├── ReadProcessPeaks.c │ ├── ReadProcessPeaksLevels.c │ ├── ReadProcessPeaksMaps.c │ ├── ReadProcessPeaksPhastCons.c │ ├── ReadRefgeneFile.c │ ├── ReadRefgeneFile2.c │ ├── ReadRefgeneFileMark.c │ ├── ReadRefgeneFileMarkExons.c │ ├── ReadSAMFile.c │ ├── ReadWIGFile.c │ ├── RequestMemory.c │ ├── RequestMemoryBin.c │ ├── account.c │ ├── buildChIPprofile.c │ ├── combineChIPprofiles.c │ ├── combineTSSmaps.c │ ├── combineTSSplots.c │ ├── computemaxsignal.c │ ├── findPeaks.c │ ├── genomeDistribution.c │ ├── matchpeaks.c │ ├── matchpeaksgenes.c │ ├── processmacs.c │ ├── produceGENEmaps.c │ ├── produceGENEplots.c │ ├── producePEAKmaps.c │ ├── producePEAKplots.c │ ├── produceTESmaps.c │ ├── produceTESplots.c │ ├── produceTSSmaps.c │ ├── produceTSSplots.c │ ├── readargv_buildChIPprofile.c │ ├── readargv_combineChIPprofiles.c │ ├── readargv_combineTSSmaps.c │ ├── readargv_combineTSSplots.c │ ├── readargv_computemaxsignal.c │ ├── readargv_findPeaks.c │ ├── readargv_genomeDistribution.c │ ├── readargv_matchpeaks.c │ ├── readargv_matchpeaksgenes.c │ ├── readargv_processmacs.c │ ├── readargv_produceGENEmaps.c │ ├── readargv_produceGENEplots.c │ ├── readargv_producePEAKmaps.c │ ├── readargv_producePEAKplots.c │ ├── readargv_produceTESmaps.c │ ├── readargv_produceTESplots.c │ ├── readargv_produceTSSmaps.c │ ├── readargv_produceTSSplots.c │ ├── readargv_recoverChIPlevels.c │ ├── readargv_scorePhastCons.c │ ├── recoverChIPlevels.c │ └── scorePhastCons.c └── tests ├── finaloutputs ├── buildChIPprofile │ ├── test_1_BedGraph_profile │ │ └── test_1.bedgraph.gz │ ├── test_2_BedGraph_profile │ │ └── test_2.bedgraph.gz │ └── test_3_BedGraph_profile │ │ └── test_3.bedgraph.gz ├── combineChIPprofiles │ ├── test_1_BedGraph_profile │ │ └── test_1.bedgraph.gz │ ├── test_2_BedGraph_profile │ │ └── test_2.bedgraph.gz │ └── test_3-test_3_BedGraph_profile │ │ └── test_3-test_3.bedgraph.gz ├── combineTSSplots │ ├── combineTSS2plots.pdf │ ├── test_1_TSSplot_5000 │ │ ├── PlotTSSprofile_test_1_5000.pdf │ │ ├── RscriptTSSprofile_test_1_5000.txt │ │ └── TSSprofile_test_1_5000.txt │ ├── test_2_TSSplot_5000 │ │ ├── PlotTSSprofile_test_2_5000.pdf │ │ ├── RscriptTSSprofile_test_2_5000.txt │ │ └── TSSprofile_test_2_5000.txt │ ├── test_3-test_3_TSSplot_5000 │ │ ├── PlotTSSprofile_test_3-test_3_5000.pdf │ │ ├── RscriptTSSprofile_test_3-test_3_5000.txt │ │ └── TSSprofile_test_3-test_3_5000.txt │ ├── test_4_TSSplot_5000 │ │ ├── PlotTSSprofile_test_4_5000.pdf │ │ ├── RscriptTSSprofile_test_4_5000.txt │ │ └── TSSprofile_test_4_5000.txt │ ├── test_5_TSSplot_5000 │ │ ├── PlotTSSprofile_test_5_5000.pdf │ │ ├── RscriptTSSprofile_test_5_5000.txt │ │ └── TSSprofile_test_5_5000.txt │ └── test_6-test_6_TSSplot_5000 │ │ ├── PlotTSSprofile_test_6-test_6_5000.pdf │ │ ├── RscriptTSSprofile_test_6-test_6_5000.txt │ │ └── TSSprofile_test_6-test_6_5000.txt ├── findPeaks │ ├── test_1_findPeaks │ │ └── test_1.bed.gz │ └── test_2_findPeaks │ │ └── test_2.bed.gz ├── genomeDistribution │ ├── test_1_GENOMEchart │ │ ├── GENOMEchart_test_1.txt │ │ ├── PlotGENOMEchart_test_1.pdf │ │ └── RscriptGENOMEchart_test_1.txt │ ├── test_2_GENOMEchart │ │ ├── GENOMEchart_test_2.txt │ │ ├── PlotGENOMEchart_test_2.pdf │ │ └── RscriptGENOMEchart_test_2.txt │ ├── test_3_GENOMEchart │ │ ├── GENOMEchart_test_3.txt │ │ ├── PlotGENOMEchart_test_3.pdf │ │ └── RscriptGENOMEchart_test_3.txt │ ├── test_4_GENOMEchart │ │ ├── GENOMEchart_test_4.txt │ │ ├── PlotGENOMEchart_test_4.pdf │ │ └── RscriptGENOMEchart_test_4.txt │ ├── test_5_GENOMEchart │ │ ├── GENOMEchart_test_5.txt │ │ ├── PlotGENOMEchart_test_5.pdf │ │ └── RscriptGENOMEchart_test_5.txt │ ├── test_6_GENOMEchart │ │ ├── GENOMEchart_test_6.txt │ │ ├── PlotGENOMEchart_test_6.pdf │ │ └── RscriptGENOMEchart_test_6.txt │ ├── test_7_GENOMEchart │ │ ├── GENOMEchart_test_7.txt │ │ ├── PlotGENOMEchart_test_7.pdf │ │ └── RscriptGENOMEchart_test_7.txt │ └── test_8_GENOMEchart │ │ ├── GENOMEchart_test_8.txt │ │ ├── PlotGENOMEchart_test_8.pdf │ │ └── RscriptGENOMEchart_test_8.txt ├── matchpeaks │ ├── test_1A_test_1B_matchpeaks │ │ ├── common_test_1A_test_1B.bed │ │ ├── mystderr.txt │ │ ├── only_test_1A.bed │ │ └── only_test_1B.bed │ └── test_2A_test_2B_matchpeaks │ │ ├── common_test_2A_test_2B.bed │ │ ├── mystderr.txt │ │ ├── only_test_2A.bed │ │ └── only_test_2B.bed ├── matchpeaksgenes │ ├── test_1.txt │ ├── test_12_genes.txt │ ├── test_1_genes.txt │ ├── test_2.txt │ ├── test_2_genes.txt │ ├── test_3.txt │ ├── test_34_genes.txt │ ├── test_3_genes.txt │ ├── test_4.txt │ └── test_4_genes.txt ├── produceGENEmaps │ ├── produceGENE2maps.pdf │ ├── test_1_GENEmap_5000 │ │ ├── HEATmatrix_test_1_5000.txt │ │ ├── HEATmatrix_test_1_5000_genes.txt │ │ ├── HEATmatrix_test_1_5000_processed.txt │ │ ├── PlotHEATmap_test_1_5000.pdf │ │ └── RscriptGENEmap_test_1_5000.txt │ ├── test_2_GENEmap_5000 │ │ ├── HEATmatrix_test_2_5000.txt │ │ ├── HEATmatrix_test_2_5000_genes.txt │ │ ├── HEATmatrix_test_2_5000_processed.txt │ │ ├── PlotHEATmap_test_2_5000.pdf │ │ └── RscriptGENEmap_test_2_5000.txt │ ├── test_3_GENEmap_5000 │ │ ├── HEATmatrix_test_3_5000.txt │ │ ├── HEATmatrix_test_3_5000_genes.txt │ │ ├── HEATmatrix_test_3_5000_processed.txt │ │ ├── PlotHEATmap_test_3_5000.pdf │ │ └── RscriptGENEmap_test_3_5000.txt │ ├── test_4_GENEmap_5000 │ │ ├── HEATmatrix_test_4_5000.txt │ │ ├── HEATmatrix_test_4_5000_genes.txt │ │ ├── HEATmatrix_test_4_5000_processed.txt │ │ ├── PlotHEATmap_test_4_5000.pdf │ │ └── RscriptGENEmap_test_4_5000.txt │ ├── test_5_GENEmap_5000 │ │ ├── HEATmatrix_test_5_5000.txt │ │ ├── HEATmatrix_test_5_5000_genes.txt │ │ ├── HEATmatrix_test_5_5000_processed.txt │ │ ├── PlotHEATmap_test_5_5000.pdf │ │ └── RscriptGENEmap_test_5_5000.txt │ ├── test_6_GENEmap_5000 │ │ ├── HEATmatrix_test_6_5000.txt │ │ ├── HEATmatrix_test_6_5000_genes.txt │ │ ├── HEATmatrix_test_6_5000_processed.txt │ │ ├── PlotHEATmap_test_6_5000.pdf │ │ └── RscriptGENEmap_test_6_5000.txt │ └── test_7_GENEmap_5000 │ │ ├── HEATmatrix_test_7_5000.txt │ │ ├── HEATmatrix_test_7_5000_genes.txt │ │ ├── HEATmatrix_test_7_5000_processed.txt │ │ ├── PlotHEATmap_test_7_5000.pdf │ │ └── RscriptGENEmap_test_7_5000.txt ├── produceGENEplots │ ├── produceGENE2plots.pdf │ ├── test_1_GENEplot_5000 │ │ ├── GENEprofile_test_1_5000.txt │ │ ├── PlotGENEprofile_test_1_5000.pdf │ │ └── RscriptGENEprofile_test_1_5000.txt │ ├── test_2_GENEplot_5000 │ │ ├── GENEprofile_test_2_5000.txt │ │ ├── PlotGENEprofile_test_2_5000.pdf │ │ └── RscriptGENEprofile_test_2_5000.txt │ ├── test_3_GENEplot_5000 │ │ ├── GENEprofile_test_3_5000.txt │ │ ├── PlotGENEprofile_test_3_5000.pdf │ │ └── RscriptGENEprofile_test_3_5000.txt │ ├── test_4_GENEplot_5000 │ │ ├── GENEprofile_test_4_5000.txt │ │ ├── PlotGENEprofile_test_4_5000.pdf │ │ └── RscriptGENEprofile_test_4_5000.txt │ ├── test_5_GENEplot_5000 │ │ ├── GENEprofile_test_5_5000.txt │ │ ├── PlotGENEprofile_test_5_5000.pdf │ │ └── RscriptGENEprofile_test_5_5000.txt │ └── test_6_GENEplot_5000 │ │ ├── GENEprofile_test_6_5000.txt │ │ ├── PlotGENEprofile_test_6_5000.pdf │ │ └── RscriptGENEprofile_test_6_5000.txt ├── producePEAKmaps │ ├── producePEAK2maps.pdf │ ├── test_1_PEAKmap_5000 │ │ ├── CenterBedPEAK_test_1_5000.bed │ │ ├── HEATmatrix_test_1_5000.txt │ │ ├── HEATmatrix_test_1_5000_peaks.txt │ │ ├── HEATmatrix_test_1_5000_processed.txt │ │ ├── PlotHEATmap_test_1_5000.pdf │ │ └── RscriptPEAKmap_test_1_5000.txt │ ├── test_2_PEAKmap_5000 │ │ ├── CenterBedPEAK_test_2_5000.bed │ │ ├── HEATmatrix_test_2_5000.txt │ │ ├── HEATmatrix_test_2_5000_peaks.txt │ │ ├── HEATmatrix_test_2_5000_processed.txt │ │ ├── PlotHEATmap_test_2_5000.pdf │ │ └── RscriptPEAKmap_test_2_5000.txt │ ├── test_3_PEAKmap_5000 │ │ ├── CenterBedPEAK_test_3_5000.bed │ │ ├── HEATmatrix_test_3_5000.txt │ │ ├── HEATmatrix_test_3_5000_peaks.txt │ │ ├── HEATmatrix_test_3_5000_processed.txt │ │ ├── PlotHEATmap_test_3_5000.pdf │ │ └── RscriptPEAKmap_test_3_5000.txt │ ├── test_4_PEAKmap_5000 │ │ ├── CenterBedPEAK_test_4_5000.bed │ │ ├── HEATmatrix_test_4_5000.txt │ │ ├── HEATmatrix_test_4_5000_peaks.txt │ │ ├── HEATmatrix_test_4_5000_processed.txt │ │ ├── PlotHEATmap_test_4_5000.pdf │ │ └── RscriptPEAKmap_test_4_5000.txt │ ├── test_5_PEAKmap_5000 │ │ ├── CenterBedPEAK_test_5_5000.bed │ │ ├── HEATmatrix_test_5_5000.txt │ │ ├── HEATmatrix_test_5_5000_peaks.txt │ │ ├── HEATmatrix_test_5_5000_processed.txt │ │ ├── PlotHEATmap_test_5_5000.pdf │ │ └── RscriptPEAKmap_test_5_5000.txt │ ├── test_6_PEAKmap_5000 │ │ ├── CenterBedPEAK_test_6_5000.bed │ │ ├── HEATmatrix_test_6_5000.txt │ │ ├── HEATmatrix_test_6_5000_peaks.txt │ │ ├── HEATmatrix_test_6_5000_processed.txt │ │ ├── PlotHEATmap_test_6_5000.pdf │ │ └── RscriptPEAKmap_test_6_5000.txt │ └── test_7_PEAKmap_5000 │ │ ├── CenterBedPEAK_test_7_5000.bed │ │ ├── HEATmatrix_test_7_5000.txt │ │ ├── HEATmatrix_test_7_5000_peaks.txt │ │ ├── HEATmatrix_test_7_5000_processed.txt │ │ ├── PlotHEATmap_test_7_5000.pdf │ │ └── RscriptPEAKmap_test_7_5000.txt ├── producePEAKplots │ ├── producePEAK2plots.pdf │ ├── test_1_PEAKplot_5000 │ │ ├── CenterBedPEAK_test_1_5000.bed │ │ ├── PEAKprofile_test_1_5000.txt │ │ ├── PlotPEAKprofile_test_1_5000.pdf │ │ └── RscriptPEAKprofile_test_1_5000.txt │ ├── test_2_PEAKplot_5000 │ │ ├── CenterBedPEAK_test_2_5000.bed │ │ ├── PEAKprofile_test_2_5000.txt │ │ ├── PlotPEAKprofile_test_2_5000.pdf │ │ └── RscriptPEAKprofile_test_2_5000.txt │ ├── test_3_PEAKplot_5000 │ │ ├── CenterBedPEAK_test_3_5000.bed │ │ ├── PEAKprofile_test_3_5000.txt │ │ ├── PlotPEAKprofile_test_3_5000.pdf │ │ └── RscriptPEAKprofile_test_3_5000.txt │ ├── test_4_PEAKplot_5000 │ │ ├── CenterBedPEAK_test_4_5000.bed │ │ ├── PEAKprofile_test_4_5000.txt │ │ ├── PlotPEAKprofile_test_4_5000.pdf │ │ └── RscriptPEAKprofile_test_4_5000.txt │ ├── test_5_PEAKplot_5000 │ │ ├── CenterBedPEAK_test_5_5000.bed │ │ ├── PEAKprofile_test_5_5000.txt │ │ ├── PlotPEAKprofile_test_5_5000.pdf │ │ └── RscriptPEAKprofile_test_5_5000.txt │ └── test_6_PEAKplot_5000 │ │ ├── CenterBedPEAK_test_6_5000.bed │ │ ├── PEAKprofile_test_6_5000.txt │ │ ├── PlotPEAKprofile_test_6_5000.pdf │ │ └── RscriptPEAKprofile_test_6_5000.txt ├── produceTSSmaps │ ├── produceTSS2maps.pdf │ ├── test_1_TSSmap_5000 │ │ ├── HEATmatrix_test_1_5000.txt │ │ ├── HEATmatrix_test_1_5000_genes.txt │ │ ├── HEATmatrix_test_1_5000_processed.txt │ │ ├── PlotHEATmap_test_1_5000.pdf │ │ └── RscriptTSSmap_test_1_5000.txt │ ├── test_2_TSSmap_5000 │ │ ├── HEATmatrix_test_2_5000.txt │ │ ├── HEATmatrix_test_2_5000_genes.txt │ │ ├── HEATmatrix_test_2_5000_processed.txt │ │ ├── PlotHEATmap_test_2_5000.pdf │ │ └── RscriptTSSmap_test_2_5000.txt │ ├── test_3_TSSmap_5000 │ │ ├── HEATmatrix_test_3_5000.txt │ │ ├── HEATmatrix_test_3_5000_genes.txt │ │ ├── HEATmatrix_test_3_5000_processed.txt │ │ ├── PlotHEATmap_test_3_5000.pdf │ │ └── RscriptTSSmap_test_3_5000.txt │ ├── test_4_TSSmap_5000 │ │ ├── HEATmatrix_test_4_5000.txt │ │ ├── HEATmatrix_test_4_5000_genes.txt │ │ ├── HEATmatrix_test_4_5000_processed.txt │ │ ├── PlotHEATmap_test_4_5000.pdf │ │ └── RscriptTSSmap_test_4_5000.txt │ ├── test_5_TSSmap_5000 │ │ ├── HEATmatrix_test_5_5000.txt │ │ ├── HEATmatrix_test_5_5000_genes.txt │ │ ├── HEATmatrix_test_5_5000_processed.txt │ │ ├── PlotHEATmap_test_5_5000.pdf │ │ └── RscriptTSSmap_test_5_5000.txt │ ├── test_6_TSSmap_5000 │ │ ├── HEATmatrix_test_6_5000.txt │ │ ├── HEATmatrix_test_6_5000_genes.txt │ │ ├── HEATmatrix_test_6_5000_processed.txt │ │ ├── PlotHEATmap_test_6_5000.pdf │ │ └── RscriptTSSmap_test_6_5000.txt │ └── test_7_TSSmap_5000 │ │ ├── HEATmatrix_test_7_5000.txt │ │ ├── HEATmatrix_test_7_5000_genes.txt │ │ ├── HEATmatrix_test_7_5000_processed.txt │ │ ├── PlotHEATmap_test_7_5000.pdf │ │ └── RscriptTSSmap_test_7_5000.txt ├── produceTSSplots │ ├── produceTSS2plots.pdf │ ├── test_1_TSSplot_5000 │ │ ├── PlotTSSprofile_test_1_5000.pdf │ │ ├── RscriptTSSprofile_test_1_5000.txt │ │ └── TSSprofile_test_1_5000.txt │ ├── test_2_TSSplot_5000 │ │ ├── PlotTSSprofile_test_2_5000.pdf │ │ ├── RscriptTSSprofile_test_2_5000.txt │ │ └── TSSprofile_test_2_5000.txt │ ├── test_3_TSSplot_5000 │ │ ├── PlotTSSprofile_test_3_5000.pdf │ │ ├── RscriptTSSprofile_test_3_5000.txt │ │ └── TSSprofile_test_3_5000.txt │ ├── test_4_TSSplot_5000 │ │ ├── PlotTSSprofile_test_4_5000.pdf │ │ ├── RscriptTSSprofile_test_4_5000.txt │ │ └── TSSprofile_test_4_5000.txt │ ├── test_5_TSSplot_5000 │ │ ├── PlotTSSprofile_test_5_5000.pdf │ │ ├── RscriptTSSprofile_test_5_5000.txt │ │ └── TSSprofile_test_5_5000.txt │ └── test_6_TSSplot_5000 │ │ ├── PlotTSSprofile_test_6_5000.pdf │ │ ├── RscriptTSSprofile_test_6_5000.txt │ │ └── TSSprofile_test_6_5000.txt └── recoverChIPlevels │ ├── recoverChIPlevels.pdf │ ├── test_1_recoverChIPlevels │ └── PEAKsignal_test_1.bed │ ├── test_2_recoverChIPlevels │ └── PEAKsignal_test_2.bed │ ├── test_3_recoverChIPlevels │ └── PEAKsignal_test_3.bed │ └── test_4_recoverChIPlevels │ └── PEAKsignal_test_4.bed ├── inputs ├── ChromInfo.txt ├── H3K27me3_chr10.bed ├── H3K27me3_mESC_sample.bed ├── H3K4me3_chr10.bed ├── H3K4me3_mESC_sample.bed ├── H3K4me3_sample.bam ├── H3_sample.bam ├── Rscript_combineTSSplots.txt ├── Rscript_produceGENEmaps.txt ├── Rscript_produceGENEplots.txt ├── Rscript_producePEAKmaps.txt ├── Rscript_producePEAKplots.txt ├── Rscript_produceTSSmaps.txt ├── Rscript_produceTSSplots.txt ├── Rscript_recoverChIPlevels.txt ├── genes_sample.txt ├── onegene.txt ├── onepeak.bed └── refGene_sample.txt ├── outputs └── .gitignore ├── test_buildChIPprofile.pl ├── test_combineChIPprofiles.pl ├── test_combineTSSplots.pl ├── test_findPeaks.pl ├── test_genomeDistribution.pl ├── test_matchpeaks.pl ├── test_matchpeaksgenes.pl ├── test_produceGENEmaps.pl ├── test_produceGENEplots.pl ├── test_producePEAKmaps.pl ├── test_producePEAKplots.pl ├── test_produceTSSmaps.pl ├── test_produceTSSplots.pl └── test_recoverChIPlevels.pl /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eblancoga/seqcode/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eblancoga/seqcode/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eblancoga/seqcode/HEAD/README.md -------------------------------------------------------------------------------- /bin/.gitignore: -------------------------------------------------------------------------------- 1 | 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