├── .gitignore ├── LICENSE ├── README.md ├── data ├── backgrounds │ └── nloci49_nperm500_kb500_rsq0.1_mhc25000000-35000000_colld0.5-collection-1000genomespilot-depict-150429 │ │ ├── permutation1.txt.gz │ │ ├── permutation10.txt.gz │ │ ├── permutation100.txt.gz │ │ ├── permutation101.txt.gz │ │ ├── permutation102.txt.gz │ │ ├── permutation103.txt.gz │ │ ├── permutation104.txt.gz │ │ ├── permutation105.txt.gz │ │ ├── permutation106.txt.gz │ │ ├── permutation107.txt.gz │ │ ├── permutation108.txt.gz │ │ ├── permutation109.txt.gz │ │ ├── permutation11.txt.gz │ │ ├── permutation110.txt.gz │ │ ├── permutation111.txt.gz │ │ ├── permutation112.txt.gz │ │ ├── permutation113.txt.gz │ │ ├── permutation114.txt.gz │ │ ├── permutation115.txt.gz │ │ ├── permutation116.txt.gz │ │ ├── permutation117.txt.gz │ │ ├── permutation118.txt.gz │ │ ├── permutation119.txt.gz │ │ ├── permutation12.txt.gz │ │ ├── permutation120.txt.gz │ │ ├── permutation121.txt.gz │ │ ├── permutation122.txt.gz │ │ ├── permutation123.txt.gz │ │ ├── permutation124.txt.gz │ │ ├── permutation125.txt.gz │ │ ├── permutation126.txt.gz │ │ ├── permutation127.txt.gz │ │ ├── permutation128.txt.gz │ │ ├── permutation129.txt.gz │ │ ├── permutation13.txt.gz │ │ ├── permutation130.txt.gz │ │ ├── permutation131.txt.gz │ │ ├── permutation132.txt.gz │ │ ├── permutation133.txt.gz │ │ ├── permutation134.txt.gz │ │ ├── permutation135.txt.gz │ │ ├── permutation136.txt.gz │ │ ├── permutation137.txt.gz │ │ ├── permutation138.txt.gz │ │ ├── permutation139.txt.gz │ │ ├── permutation14.txt.gz │ │ ├── permutation140.txt.gz │ │ ├── permutation141.txt.gz │ │ ├── permutation142.txt.gz │ │ ├── permutation143.txt.gz │ │ ├── permutation144.txt.gz │ │ ├── permutation145.txt.gz │ │ ├── permutation146.txt.gz │ │ ├── permutation147.txt.gz │ │ ├── permutation148.txt.gz │ │ ├── permutation149.txt.gz │ │ ├── permutation15.txt.gz │ │ ├── permutation150.txt.gz │ │ ├── permutation151.txt.gz │ │ ├── permutation152.txt.gz │ │ ├── permutation153.txt.gz │ │ ├── permutation154.txt.gz │ │ ├── permutation155.txt.gz │ │ ├── permutation156.txt.gz │ │ ├── permutation157.txt.gz │ │ ├── permutation158.txt.gz │ │ ├── permutation159.txt.gz │ │ ├── permutation16.txt.gz │ │ ├── permutation160.txt.gz │ │ ├── permutation161.txt.gz │ │ ├── permutation162.txt.gz │ │ ├── permutation163.txt.gz │ │ ├── permutation164.txt.gz │ │ ├── permutation165.txt.gz │ │ ├── permutation166.txt.gz │ │ ├── permutation167.txt.gz │ │ ├── permutation168.txt.gz │ │ ├── permutation169.txt.gz │ │ ├── permutation17.txt.gz │ │ ├── permutation170.txt.gz │ │ ├── permutation172.txt.gz │ │ ├── permutation173.txt.gz │ │ ├── permutation174.txt.gz │ │ ├── permutation175.txt.gz │ │ ├── permutation176.txt.gz │ │ ├── permutation177.txt.gz │ │ ├── permutation178.txt.gz │ │ ├── permutation179.txt.gz │ │ ├── permutation18.txt.gz │ │ ├── permutation180.txt.gz │ │ ├── permutation181.txt.gz │ │ ├── permutation183.txt.gz │ │ ├── permutation184.txt.gz │ │ ├── permutation185.txt.gz │ │ ├── permutation186.txt.gz │ │ ├── permutation187.txt.gz │ │ ├── permutation188.txt.gz │ │ ├── permutation189.txt.gz │ │ ├── permutation19.txt.gz │ │ ├── permutation190.txt.gz │ │ ├── permutation191.txt.gz │ │ ├── permutation192.txt.gz │ │ ├── permutation193.txt.gz │ │ ├── permutation194.txt.gz │ │ ├── permutation195.txt.gz │ │ ├── permutation196.txt.gz │ │ ├── permutation197.txt.gz │ │ ├── permutation198.txt.gz │ │ ├── permutation199.txt.gz │ │ ├── permutation2.txt.gz │ │ ├── permutation20.txt.gz │ │ ├── permutation200.txt.gz │ │ ├── permutation201.txt.gz │ │ ├── permutation202.txt.gz │ │ ├── permutation203.txt.gz │ │ ├── permutation204.txt.gz │ │ ├── permutation205.txt.gz │ │ ├── permutation206.txt.gz │ │ ├── permutation207.txt.gz │ │ ├── permutation208.txt.gz │ │ ├── permutation209.txt.gz │ │ ├── permutation21.txt.gz │ │ ├── permutation210.txt.gz │ │ ├── permutation211.txt.gz │ │ ├── permutation212.txt.gz │ │ ├── permutation213.txt.gz │ │ ├── permutation214.txt.gz │ │ ├── permutation215.txt.gz │ │ ├── permutation216.txt.gz │ │ ├── permutation217.txt.gz │ │ ├── permutation218.txt.gz │ │ ├── permutation219.txt.gz │ │ ├── permutation22.txt.gz │ │ ├── permutation220.txt.gz │ │ ├── permutation221.txt.gz │ │ ├── permutation222.txt.gz │ │ ├── permutation223.txt.gz │ │ ├── permutation224.txt.gz │ │ ├── permutation225.txt.gz │ │ ├── permutation226.txt.gz │ │ ├── permutation227.txt.gz │ │ ├── permutation228.txt.gz │ │ ├── permutation229.txt.gz │ │ ├── permutation23.txt.gz │ │ ├── permutation230.txt.gz │ │ ├── permutation231.txt.gz │ │ ├── permutation232.txt.gz │ │ ├── permutation233.txt.gz │ │ ├── permutation234.txt.gz │ │ ├── permutation235.txt.gz │ │ ├── permutation236.txt.gz │ │ ├── permutation237.txt.gz │ │ ├── permutation238.txt.gz │ │ ├── permutation239.txt.gz │ │ ├── permutation24.txt.gz │ │ ├── permutation240.txt.gz │ │ ├── permutation241.txt.gz │ │ ├── permutation242.txt.gz │ │ ├── permutation243.txt.gz │ │ ├── permutation244.txt.gz │ │ ├── permutation245.txt.gz │ │ ├── permutation246.txt.gz │ │ ├── permutation247.txt.gz │ │ ├── permutation248.txt.gz │ │ ├── permutation249.txt.gz │ │ ├── permutation25.txt.gz │ │ ├── permutation250.txt.gz │ │ ├── permutation251.txt.gz │ │ ├── permutation252.txt.gz │ │ ├── permutation253.txt.gz │ │ ├── permutation254.txt.gz │ │ ├── permutation255.txt.gz │ │ ├── permutation256.txt.gz │ │ ├── permutation257.txt.gz │ │ ├── permutation258.txt.gz │ │ ├── permutation259.txt.gz │ │ ├── permutation26.txt.gz │ │ ├── permutation260.txt.gz │ │ ├── permutation261.txt.gz │ │ ├── permutation262.txt.gz │ │ ├── permutation263.txt.gz │ │ ├── permutation264.txt.gz │ │ ├── permutation265.txt.gz │ │ ├── permutation266.txt.gz │ │ ├── permutation267.txt.gz │ │ ├── permutation268.txt.gz │ │ ├── permutation269.txt.gz │ │ ├── permutation27.txt.gz │ │ ├── permutation270.txt.gz │ │ ├── permutation271.txt.gz │ │ ├── permutation272.txt.gz │ │ ├── permutation273.txt.gz │ │ ├── permutation274.txt.gz │ │ ├── permutation275.txt.gz │ │ ├── permutation276.txt.gz │ │ ├── permutation277.txt.gz │ │ ├── permutation278.txt.gz │ │ ├── permutation279.txt.gz │ │ ├── permutation28.txt.gz │ │ ├── permutation280.txt.gz │ │ ├── permutation281.txt.gz │ │ ├── permutation282.txt.gz │ │ ├── permutation283.txt.gz │ │ ├── permutation284.txt.gz │ │ ├── permutation285.txt.gz │ │ ├── permutation286.txt.gz │ │ ├── permutation287.txt.gz │ │ ├── permutation288.txt.gz │ │ ├── permutation289.txt.gz │ │ ├── permutation29.txt.gz │ │ ├── permutation290.txt.gz │ │ ├── permutation291.txt.gz │ │ ├── permutation292.txt.gz │ │ ├── permutation293.txt.gz │ │ ├── permutation294.txt.gz │ │ ├── permutation295.txt.gz │ │ ├── permutation296.txt.gz │ │ ├── permutation297.txt.gz │ │ ├── permutation298.txt.gz │ │ ├── permutation299.txt.gz │ │ ├── permutation3.txt.gz │ │ ├── permutation30.txt.gz │ │ ├── permutation300.txt.gz │ │ ├── permutation301.txt.gz │ │ ├── permutation302.txt.gz │ │ ├── permutation303.txt.gz │ │ ├── permutation304.txt.gz │ │ ├── permutation305.txt.gz │ │ ├── permutation306.txt.gz │ │ ├── permutation307.txt.gz │ │ ├── permutation308.txt.gz │ │ ├── permutation309.txt.gz │ │ ├── permutation31.txt.gz │ │ ├── permutation310.txt.gz │ │ ├── permutation311.txt.gz │ │ ├── permutation312.txt.gz │ │ ├── permutation313.txt.gz │ │ ├── permutation314.txt.gz │ │ ├── permutation315.txt.gz │ │ ├── permutation316.txt.gz │ │ ├── permutation317.txt.gz │ │ ├── permutation318.txt.gz │ │ ├── permutation319.txt.gz │ │ ├── permutation32.txt.gz │ │ ├── permutation320.txt.gz │ │ ├── permutation321.txt.gz │ │ ├── permutation322.txt.gz │ │ ├── permutation323.txt.gz │ │ ├── permutation324.txt.gz │ │ ├── permutation325.txt.gz │ │ ├── permutation326.txt.gz │ │ ├── permutation327.txt.gz │ │ ├── permutation328.txt.gz │ │ ├── permutation329.txt.gz │ │ ├── permutation33.txt.gz │ │ ├── permutation330.txt.gz │ │ ├── permutation331.txt.gz │ │ ├── permutation332.txt.gz │ │ ├── permutation333.txt.gz │ │ ├── permutation334.txt.gz │ │ ├── permutation335.txt.gz │ │ ├── permutation336.txt.gz │ │ ├── permutation337.txt.gz │ │ ├── permutation338.txt.gz │ │ ├── permutation339.txt.gz │ │ ├── permutation34.txt.gz │ │ ├── permutation340.txt.gz │ │ ├── permutation341.txt.gz │ │ ├── permutation342.txt.gz │ │ ├── permutation343.txt.gz │ │ ├── permutation344.txt.gz │ │ ├── permutation345.txt.gz │ │ ├── permutation346.txt.gz │ │ ├── permutation347.txt.gz │ │ ├── permutation348.txt.gz │ │ ├── permutation349.txt.gz │ │ ├── permutation35.txt.gz │ │ ├── permutation350.txt.gz │ │ ├── permutation351.txt.gz │ │ ├── permutation352.txt.gz │ │ ├── permutation353.txt.gz │ │ ├── permutation354.txt.gz │ │ ├── permutation355.txt.gz │ │ ├── permutation356.txt.gz │ │ ├── permutation357.txt.gz │ │ ├── permutation358.txt.gz │ │ ├── permutation359.txt.gz │ │ ├── permutation36.txt.gz │ │ ├── permutation360.txt.gz │ │ ├── permutation361.txt.gz │ │ ├── permutation362.txt.gz │ │ ├── permutation363.txt.gz │ │ ├── permutation364.txt.gz │ │ ├── permutation365.txt.gz │ │ ├── permutation366.txt.gz │ │ ├── permutation367.txt.gz │ │ ├── permutation368.txt.gz │ │ ├── permutation369.txt.gz │ │ ├── permutation37.txt.gz │ │ ├── permutation370.txt.gz │ │ ├── permutation371.txt.gz │ │ ├── permutation372.txt.gz │ │ ├── permutation373.txt.gz │ │ ├── permutation374.txt.gz │ │ ├── permutation375.txt.gz │ │ ├── permutation376.txt.gz │ │ ├── permutation377.txt.gz │ │ ├── permutation378.txt.gz │ │ ├── permutation379.txt.gz │ │ ├── permutation38.txt.gz │ │ ├── permutation380.txt.gz │ │ ├── permutation381.txt.gz │ │ ├── permutation382.txt.gz │ │ ├── permutation383.txt.gz │ │ ├── permutation384.txt.gz │ │ ├── permutation385.txt.gz │ │ ├── permutation386.txt.gz │ │ ├── permutation387.txt.gz │ │ ├── permutation388.txt.gz │ │ ├── permutation389.txt.gz │ │ ├── permutation39.txt.gz │ │ ├── permutation390.txt.gz │ │ ├── permutation391.txt.gz │ │ ├── permutation392.txt.gz │ │ ├── permutation393.txt.gz │ │ ├── permutation394.txt.gz │ │ ├── permutation395.txt.gz │ │ ├── permutation396.txt.gz │ │ ├── permutation397.txt.gz │ │ ├── permutation398.txt.gz │ │ ├── permutation399.txt.gz │ │ ├── permutation4.txt.gz │ │ ├── permutation40.txt.gz │ │ ├── permutation400.txt.gz │ │ ├── permutation401.txt.gz │ │ ├── permutation402.txt.gz │ │ ├── permutation403.txt.gz │ │ ├── permutation404.txt.gz │ │ ├── permutation405.txt.gz │ │ ├── permutation406.txt.gz │ │ ├── permutation407.txt.gz │ │ ├── permutation408.txt.gz │ │ ├── permutation409.txt.gz │ │ ├── permutation41.txt.gz │ │ ├── permutation410.txt.gz │ │ ├── permutation411.txt.gz │ │ ├── permutation412.txt.gz │ │ ├── permutation413.txt.gz │ │ ├── permutation414.txt.gz │ │ ├── permutation415.txt.gz │ │ ├── permutation416.txt.gz │ │ ├── permutation417.txt.gz │ │ ├── permutation418.txt.gz │ │ ├── permutation419.txt.gz │ │ ├── permutation42.txt.gz │ │ ├── permutation420.txt.gz │ │ ├── permutation421.txt.gz │ │ ├── permutation422.txt.gz │ │ ├── permutation423.txt.gz │ │ ├── permutation424.txt.gz │ │ ├── permutation425.txt.gz │ │ ├── permutation426.txt.gz │ │ ├── permutation427.txt.gz │ │ ├── permutation428.txt.gz │ │ ├── permutation429.txt.gz │ │ ├── permutation43.txt.gz │ │ ├── permutation430.txt.gz │ │ ├── permutation431.txt.gz │ │ ├── permutation432.txt.gz │ │ ├── permutation433.txt.gz │ │ ├── permutation434.txt.gz │ │ ├── permutation435.txt.gz │ │ ├── permutation436.txt.gz │ │ ├── permutation437.txt.gz │ │ ├── permutation438.txt.gz │ │ ├── permutation439.txt.gz │ │ ├── permutation44.txt.gz │ │ ├── permutation440.txt.gz │ │ ├── permutation441.txt.gz │ │ ├── permutation442.txt.gz │ │ ├── permutation443.txt.gz │ │ ├── permutation444.txt.gz │ │ ├── permutation445.txt.gz │ │ ├── permutation446.txt.gz │ │ ├── permutation447.txt.gz │ │ ├── permutation448.txt.gz │ │ ├── permutation449.txt.gz │ │ ├── permutation45.txt.gz │ │ ├── permutation450.txt.gz │ │ ├── permutation451.txt.gz │ │ ├── permutation452.txt.gz │ │ ├── permutation453.txt.gz │ │ ├── permutation454.txt.gz │ │ ├── permutation455.txt.gz │ │ ├── permutation456.txt.gz │ │ ├── permutation457.txt.gz │ │ ├── permutation458.txt.gz │ │ ├── permutation459.txt.gz │ │ ├── permutation46.txt.gz │ │ ├── permutation460.txt.gz │ │ ├── permutation461.txt.gz │ │ ├── permutation462.txt.gz │ │ ├── permutation463.txt.gz │ │ ├── permutation464.txt.gz │ │ ├── permutation465.txt.gz │ │ ├── permutation466.txt.gz │ │ ├── permutation467.txt.gz │ │ ├── permutation468.txt.gz │ │ ├── permutation469.txt.gz │ │ ├── permutation47.txt.gz │ │ ├── permutation470.txt.gz │ │ ├── permutation471.txt.gz │ │ ├── permutation472.txt.gz │ │ ├── permutation473.txt.gz │ │ ├── permutation474.txt.gz │ │ ├── permutation475.txt.gz │ │ ├── permutation476.txt.gz │ │ ├── permutation477.txt.gz │ │ ├── permutation478.txt.gz │ │ ├── permutation479.txt.gz │ │ ├── permutation48.txt.gz │ │ ├── permutation480.txt.gz │ │ ├── permutation481.txt.gz │ │ ├── permutation482.txt.gz │ │ ├── permutation483.txt.gz │ │ ├── permutation484.txt.gz │ │ ├── permutation485.txt.gz │ │ ├── permutation486.txt.gz │ │ ├── permutation487.txt.gz │ │ ├── permutation488.txt.gz │ │ ├── permutation489.txt.gz │ │ ├── permutation49.txt.gz │ │ ├── permutation490.txt.gz │ │ ├── permutation491.txt.gz │ │ ├── permutation492.txt.gz │ │ ├── permutation493.txt.gz │ │ ├── permutation494.txt.gz │ │ ├── permutation495.txt.gz │ │ ├── permutation496.txt.gz │ │ ├── permutation497.txt.gz │ │ ├── permutation498.txt.gz │ │ ├── permutation499.txt.gz │ │ ├── permutation5.txt.gz │ │ ├── permutation50.txt.gz │ │ ├── permutation500.txt.gz │ │ ├── permutation51.txt.gz │ │ ├── permutation52.txt.gz │ │ ├── permutation53.txt.gz │ │ ├── permutation54.txt.gz │ │ ├── permutation55.txt.gz │ │ ├── permutation56.txt.gz │ │ ├── permutation58.txt.gz │ │ ├── permutation59.txt.gz │ │ ├── permutation6.txt.gz │ │ ├── permutation60.txt.gz │ │ ├── permutation61.txt.gz │ │ ├── permutation62.txt.gz │ │ ├── permutation63.txt.gz │ │ ├── permutation64.txt.gz │ │ ├── permutation65.txt.gz │ │ ├── permutation66.txt.gz │ │ ├── permutation67.txt.gz │ │ ├── permutation68.txt.gz │ │ ├── permutation7.txt.gz │ │ ├── permutation70.txt.gz │ │ ├── permutation72.txt.gz │ │ ├── permutation73.txt.gz │ │ ├── permutation74.txt.gz │ │ ├── permutation75.txt.gz │ │ ├── permutation76.txt.gz │ │ ├── permutation77.txt.gz │ │ ├── permutation78.txt.gz │ │ ├── permutation79.txt.gz │ │ ├── permutation8.txt.gz │ │ ├── permutation80.txt.gz │ │ ├── permutation81.txt.gz │ │ ├── permutation82.txt.gz │ │ ├── permutation83.txt.gz │ │ ├── permutation84.txt.gz │ │ ├── permutation85.txt.gz │ │ ├── permutation86.txt.gz │ │ ├── permutation87.txt.gz │ │ ├── permutation88.txt.gz │ │ ├── permutation89.txt.gz │ │ ├── permutation9.txt.gz │ │ ├── permutation90.txt.gz │ │ ├── permutation91.txt.gz │ │ ├── permutation92.txt.gz │ │ ├── permutation93.txt.gz │ │ ├── permutation94.txt.gz │ │ ├── permutation95.txt.gz │ │ ├── permutation96.txt.gz │ │ ├── permutation97.txt.gz │ │ ├── permutation98.txt.gz │ │ └── permutation99.txt.gz ├── genotype_data_plink │ ├── CEU_GBR_TSI_unrelated.phase1_release_v3.20101123.snps_indels_svs.genotypes_ldl_teslovich_nature2010.bed │ ├── CEU_GBR_TSI_unrelated.phase1_release_v3.20101123.snps_indels_svs.genotypes_ldl_teslovich_nature2010.bim │ ├── CEU_GBR_TSI_unrelated.phase1_release_v3.20101123.snps_indels_svs.genotypes_ldl_teslovich_nature2010.fam │ ├── CEU_GBR_TSI_unrelated.phase1_release_v3.20101123.snps_indels_svs.genotypes_ldl_teslovich_nature2010.log │ └── CEU_GBR_TSI_unrelated.phase1_release_v3.20101123.snps_indels_svs.genotypes_ldl_teslovich_nature2010.nosex ├── mapping_and_annotation_files │ ├── 2012-08-08-IlluminaAll96PercentIdentity-ProbeAnnotation-ProbesWithWrongMappingLengthFilteredOut-EnsemblAnnotation.txt │ ├── GO.terms_alt_ids_withoutheader.tab │ ├── GPL570ProbeENSGInfo+HGNC_reformatted.txt │ ├── VOC_MammalianPhenotype.rpt │ ├── eQTLProbesFDR0.05.txt │ └── inweb_mapping.tab ├── misc │ └── genesets_to_be_excluded_lt0-01.tab └── reconstituted_genesets │ └── reconstituted_genesets_example.txt ├── example ├── ldl_teslovich_nature2010.cfg ├── ldl_teslovich_nature2010.txt.gz ├── ldl_teslovich_nature2010_depict.tab ├── ldl_teslovich_nature2010_geneprioritization.txt ├── ldl_teslovich_nature2010_genesetenrichment.txt ├── ldl_teslovich_nature2010_loci.txt ├── ldl_teslovich_nature2010_log.txt ├── ldl_teslovich_nature2010_tissue_plot │ ├── tissue_plot_genenetwork_cells.pdf │ ├── tissue_plot_genenetwork_multiplot.pdf │ ├── tissue_plot_genenetwork_system.pdf │ ├── tissue_plot_genenetwork_tissues.pdf │ └── tissue_plot_gtex.pdf ├── ldl_teslovich_nature2010_tissueenrichment.txt └── ldl_teslovich_nature2010_tissueenrichment_gtex.txt └── src ├── java ├── build.xml ├── build │ ├── built-jar.properties │ └── classes │ │ └── depict │ │ ├── DEPICT.class │ │ ├── PerformNetworkAnalysisSusceptibilityLociPermutationTask.class │ │ ├── PerformPathwayAnalysisSusceptibilityLoci.class │ │ ├── PerformPathwayAnalysisSusceptibilityLociPermutationTask.class │ │ ├── PredictGenesetMemberBasedOnTCs.class │ │ ├── Testing.class │ │ ├── math │ │ ├── DoubleDoubleObject.class │ │ ├── DoubleDoubleObjectSorter.class │ │ ├── IntegerDoubleObject.class │ │ ├── StringDoubleObject.class │ │ ├── StringDoubleObjectSorter.class │ │ ├── StringIntegerObject.class │ │ ├── StringIntegerObjectSorter.class │ │ ├── StringIntegerObjectSorterOnIntegerValues.class │ │ ├── VectorSorter.class │ │ └── WilcoxonMannWhitney.class │ │ └── matrix │ │ ├── ExpressionDataset.class │ │ └── SymmetricShortDistanceMatrix.class ├── dist │ ├── Depict.jar │ ├── README.TXT │ └── lib │ │ ├── Jama-1.0.2.jar │ │ ├── colt.jar │ │ ├── commons-math-2.0.jar │ │ ├── jsc.jar │ │ ├── jsci-core.jar │ │ └── jscicore.jar ├── lib │ ├── JSciCore.jar │ ├── Jama-1.0.2.jar │ ├── colt.jar │ ├── commons-math-2.0.jar │ ├── jsc.jar │ ├── jsci-core.jar │ └── l ├── manifest.mf ├── nbproject │ ├── build-impl.xml │ ├── genfiles.properties │ ├── private │ │ ├── config.properties │ │ ├── private.properties │ │ └── private.xml │ ├── project.properties │ └── project.xml └── src │ └── depict │ ├── DEPICT.java │ ├── PerformNetworkAnalysisSusceptibilityLociPermutationTask.java │ ├── PerformPathwayAnalysisSusceptibilityLoci.java │ ├── PerformPathwayAnalysisSusceptibilityLociPermutationTask.java │ ├── PredictGenesetMemberBasedOnTCs.java │ ├── Testing.java │ ├── math │ ├── DoubleDoubleObject.java │ ├── DoubleDoubleObjectSorter.java │ ├── IntegerDoubleObject.java │ ├── StringDoubleObject.java │ ├── StringDoubleObjectSorter.java │ ├── StringIntegerObject.java │ ├── StringIntegerObjectSorter.java │ ├── StringIntegerObjectSorterOnIntegerValues.java │ ├── VectorSorter.java │ └── WilcoxonMannWhitney.java │ └── matrix │ ├── ExpressionDataset.java │ └── SymmetricShortDistanceMatrix.java └── python ├── broad_run.sh ├── depict.py ├── depict_library.py ├── example_collection.py ├── example_geno_data.sh ├── example_snp_data.py ├── network_plot.cfg ├── network_plot.py ├── network_plot_CytoscapeStyle_v1.xml ├── rm.py ├── seed_genes_ranksum.py ├── snpsnap_to_depict_collection.py ├── template.cfg └── tissue_plot.R /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/perslab/depict/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/perslab/depict/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/perslab/depict/HEAD/README.md -------------------------------------------------------------------------------- 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