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PAPER_DATA,Gene.expression.by.SNP.genotype,IBD Networks,IBD Datasets,CERTIFI DNA,Code
Gene.expression.by.SNP.genotype,CERTIFI,MSH,RISK,IBD.GPS_SNP_HLA.subtypes_coefficients_with_risk_allele_frequencies.xlsx,score_density.png
IBD.GPS_SNP_HLA.subtypes_coefficients_with_risk_allele_frequencies.xlsx
score_density.png
CERTIFI,genotype_EAF.xls,stats.xls
genotype_EAF.xls
stats.xls
MSH,genotype_EAF.xls,stats.xls
RISK,genotype_EAF.xls,stats.xls
IBD Networks,Co-expressionnetworks,Bayesiannetworks
Co-expressionnetworks,Celltype_Enrichment,Release Modules,MSigDB_Enrichment,Ontology Analysis,GO_TermEnrichment,IBD_T26_expression_Module-Trait-Correlations
Celltype_Enrichment,intersect_MSH2_ileum_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls,intersect_RISK-filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls,intersect_MSH2_colon_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls,intersect_RISK-filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls,intersect_ALL_MSH2_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls,intersect_ALL_MSH2_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls,intersect_T26-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls,intersect_MSH2_colon_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls,intersect_MSH2_ileum_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls,intersect_T26-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls,intersect_RISK-filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls,intersect_ALL_MSH2_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls,intersect_MSH2_colon_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls,intersect_MSH2_ileum_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls,intersect_T26-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls,intersect_MSH2_colon_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls,intersect_MSH2_ileum_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls,intersect_ALL_MSH2_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls,intersect_T26-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls,intersect_RISK-filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
intersect_MSH2_ileum_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls
intersect_RISK-filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls
intersect_MSH2_colon_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls
intersect_RISK-filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls
intersect_ALL_MSH2_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls
intersect_ALL_MSH2_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
intersect_T26-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls
intersect_MSH2_colon_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
intersect_MSH2_ileum_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls
intersect_T26-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls
intersect_RISK-filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls
intersect_ALL_MSH2_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls
intersect_MSH2_colon_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls
intersect_MSH2_ileum_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
intersect_T26-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls
intersect_MSH2_colon_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls
intersect_MSH2_ileum_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls
intersect_ALL_MSH2_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls
intersect_T26-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
intersect_RISK-filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
Release Modules,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-ileum_imgHierModLabeled.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex-Rgn_ALL_imgHierModules.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-ileum_imgHierClust.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-colon_imgHierClust.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_UC-colon_imgHierModules.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex-Rgn_ALL_imgHeatmap.png,IBD_risk_FPKMexpressionValues_filtered_imgHierModLabeled.png,IBD_risk_FPKMexpressionValues_filtered_imgHierModules.png,IBD_T26_expression_imgHierModules.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-colon_imgHierModLabeled.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-colon_imgHierClust.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-colon_tommodules.xls,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-ileum_imgHeatmap.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-ileum_imgHierModLabeled.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-ileum_imgHierModules.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-colon_tommodules.xls,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_UC-colon_imgHeatmap.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_UC-colon_imgHierClust.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex-Rgn_ALL_imgHierClust.png,IBD_risk_FPKMexpressionValues_filtered_tommodules.xls,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-ileum_imgHeatmap.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-colon_imgHeatmap.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex-Rgn_ALL_tommodules.xls,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_UC-colon_tommodules.xls,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-colon_imgHeatmap.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-colon_imgHierModLabeled.png,IBD_risk_FPKMexpressionValues_filtered_imgHeatmap.png,IBD_T26_expression_tommodules.xls,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-ileum_tommodules.xls,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-colon_imgHierModules.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex-Rgn_ALL_imgHierModLabeled.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-ileum_tommodules.xls,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-ileum_imgHierClust.png,IBD_T26_expression_imgHierModLabeled.png,IBD_T26_expression_imgHeatmap.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_UC-colon_imgHierModLabeled.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-ileum_imgHierModules.png,msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-colon_imgHierModules.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-ileum_imgHierModLabeled.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex-Rgn_ALL_imgHierModules.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-ileum_imgHierClust.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-colon_imgHierClust.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_UC-colon_imgHierModules.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex-Rgn_ALL_imgHeatmap.png
IBD_risk_FPKMexpressionValues_filtered_imgHierModLabeled.png
IBD_risk_FPKMexpressionValues_filtered_imgHierModules.png
IBD_T26_expression_imgHierModules.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-colon_imgHierModLabeled.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-colon_imgHierClust.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-colon_tommodules.xls
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-ileum_imgHeatmap.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-ileum_imgHierModLabeled.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-ileum_imgHierModules.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-colon_tommodules.xls
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_UC-colon_imgHeatmap.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_UC-colon_imgHierClust.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex-Rgn_ALL_imgHierClust.png
IBD_risk_FPKMexpressionValues_filtered_tommodules.xls
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-ileum_imgHeatmap.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-colon_imgHeatmap.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex-Rgn_ALL_tommodules.xls
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_UC-colon_tommodules.xls
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-colon_imgHeatmap.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-colon_imgHierModLabeled.png
IBD_risk_FPKMexpressionValues_filtered_imgHeatmap.png
IBD_T26_expression_tommodules.xls
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-ileum_tommodules.xls
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-colon_imgHierModules.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex-Rgn_ALL_imgHierModLabeled.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-ileum_tommodules.xls
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-ileum_imgHierClust.png
IBD_T26_expression_imgHierModLabeled.png
IBD_T26_expression_imgHeatmap.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_UC-colon_imgHierModLabeled.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CL-ileum_imgHierModules.png
msbb-ibd_ucsc-clean-normed_GeneWManyZerosRemoved_Adj-Age-Sex_CD-colon_imgHierModules.png
MSigDB_Enrichment,IBD_risk_processed-expression-dataT_tommodules_Ontology.xls,IBD_MSH2_ucsc-Clean_filtered_tommodules_Ontology.xls,IBD_T26_expression_tommodules2_Ontology.xls,IBD_MSH2_ucsc-Clean_ileum_filtered_tommodules_Ontology.xls,IBD_MSH2_ucsc-Clean_colon_filtered_tommodules_Ontology.xls
IBD_risk_processed-expression-dataT_tommodules_Ontology.xls
IBD_MSH2_ucsc-Clean_filtered_tommodules_Ontology.xls
IBD_T26_expression_tommodules2_Ontology.xls
IBD_MSH2_ucsc-Clean_ileum_filtered_tommodules_Ontology.xls
IBD_MSH2_ucsc-Clean_colon_filtered_tommodules_Ontology.xls
Ontology Analysis,IBD_MSH2_ucsc-Clean_ileum_filtered_tommodules_OntologyTop10-sortByModule.xls,IBD_MSH2_ucsc-Clean_colon_filtered_tommodules_OntologyTop10-sortByModule.xls,IBD_MSH2_ucsc-Clean_filtered_tommodules_OntologyTop10-sortByModule.xls,IBD_T26_expression_tommodules2_OntologyTop10-sortByModule.xls,IBD_risk_FPKMexpressionValues_filtered_tommodules_OntologyTop10-sortByModule.xls
IBD_MSH2_ucsc-Clean_ileum_filtered_tommodules_OntologyTop10-sortByModule.xls
IBD_MSH2_ucsc-Clean_colon_filtered_tommodules_OntologyTop10-sortByModule.xls
IBD_MSH2_ucsc-Clean_filtered_tommodules_OntologyTop10-sortByModule.xls
IBD_T26_expression_tommodules2_OntologyTop10-sortByModule.xls
IBD_risk_FPKMexpressionValues_filtered_tommodules_OntologyTop10-sortByModule.xls
GO_TermEnrichment,IBD_risk_processed-expression-dataT_tommodules_Ontology.xls,IBD_MSH2_ucsc-Clean_filtered_tommodules_Ontology.xls,IBD_T26_expression_tommodules2_Ontology.xls,IBD_MSH2_ucsc-Clean_ileum_filtered_tommodules_Ontology.xls,IBD_MSH2_ucsc-Clean_colon_filtered_tommodules_Ontology.xls
IBD_T26_expression_Module-Trait-Correlations,IBD_T26_expression_tommodules_aPC-GS-pval.xls,IBD_T26_expression_tommodules_aPC-GS.xls,IBD_T26_expression_tommodules_aPC-GS-fdr.xls
IBD_T26_expression_tommodules_aPC-GS-pval.xls
IBD_T26_expression_tommodules_aPC-GS.xls
IBD_T26_expression_tommodules_aPC-GS-fdr.xls
Bayesiannetworks,revisedpediatricnetwork.cys,originalimmunenetwork.cys,revisedMSHadvancednetwork.cys,revisedCERTIFImodantiTNFrefractory.cys
revisedpediatricnetwork.cys
originalimmunenetwork.cys
revisedMSHadvancednetwork.cys
revisedCERTIFImodantiTNFrefractory.cys
IBD Datasets,Gene expression by SNP genotype,Macrophagesignatures,IBDclinicalcorrelationDEsignatures
Gene expression by SNP genotype,IBD_PGS_based_on_SNPs_for_RISK_and_CERTIFI_studies
IBD_PGS_based_on_SNPs_for_RISK_and_CERTIFI_studies
Macrophagesignatures,MSG_signature.txt,MSS_signature.txt
MSG_signature.txt
MSS_signature.txt
IBDclinicalcorrelationDEsignatures,CERTIFI-Lactoferrin-.2+.2.txt,CERTIFI-FCal.txt,MSSMintestinepathscorecorr.txt,CERTIFI-Lactoferrin2.txt,MSH-UCvsCLcolon-DE.txt,CERTIFI-Diseaseduration.txt,CERTIFI-CRP.txt,CERTIFI-FCal-.3+.3.txt,MSH-CDvsCLcolon-DE.txt,MSH-CDvsUCcolon-DE.txt
CERTIFI-Lactoferrin-.2+.2.txt
CERTIFI-FCal.txt
MSSMintestinepathscorecorr.txt
CERTIFI-Lactoferrin2.txt
MSH-UCvsCLcolon-DE.txt
CERTIFI-Diseaseduration.txt
CERTIFI-CRP.txt
CERTIFI-FCal-.3+.3.txt
MSH-CDvsCLcolon-DE.txt
MSH-CDvsUCcolon-DE.txt
CERTIFI DNA,plink.fam,plink.bed,plink.bim
plink.fam
plink.bed
plink.bim
Code,enrichment,PatientDEsignatures,MouseDEsignatures,eQTL,Macrophage,GWASmapandIAMKDG,CREenrich,TF,analysis,Network
enrichment
PatientDEsignatures,ChipAnnotation.RData,DiffExpAnalysisV2.R,ProcFxns.R,BiopsyT26geneExp_wk0.RData,DiffExpAnalysisV2.RData,SummarizeResults20160309.R
ChipAnnotation.RData
DiffExpAnalysisV2.R
ProcFxns.R
BiopsyT26geneExp_wk0.RData
DiffExpAnalysisV2.RData
SummarizeResults20160309.R
MouseDEsignatures,gene_raw_counts_matrix2,ensmusg_genesymbol
gene_raw_counts_matrix2
ensmusg_genesymbol
eQTL,gt,adj.gex,code,input dataset,chr14.dose.txt.gz
chr14.dose.txt.gz
gt,step.5.impute.dose.matrix,eQTL-tools.imputed.SNP.anno
step.5.impute.dose.matrix,chr16.dose.txt.gz,chr8.dose.txt.gz,chr2.dose.txt.gz,chr18.dose.txt.gz,chr9.dose.txt.gz,chr19.dose.txt.gz,chr10.dose.txt.gz,chr13.dose.txt.gz,chr7.dose.txt.gz,chr22.dose.txt.gz,chr17.dose.txt.gz,chr6.dose.txt.gz,chr12.dose.txt.gz,chr21.dose.txt.gz,chr15.dose.txt.gz,chr20.dose.txt.gz,chr1.dose.txt.gz,chr14.dose.txt.gz,chr4.dose.txt.gz,chr11.dose.txt.gz,chr3.dose.txt.gz,chr5.dose.txt.gz
chr16.dose.txt.gz
chr8.dose.txt.gz
chr2.dose.txt.gz
chr18.dose.txt.gz
chr9.dose.txt.gz
chr19.dose.txt.gz
chr10.dose.txt.gz
chr13.dose.txt.gz
chr7.dose.txt.gz
chr22.dose.txt.gz
chr17.dose.txt.gz
chr6.dose.txt.gz
chr12.dose.txt.gz
chr21.dose.txt.gz
chr15.dose.txt.gz
chr20.dose.txt.gz
chr1.dose.txt.gz
chr4.dose.txt.gz
chr11.dose.txt.gz
chr3.dose.txt.gz
chr5.dose.txt.gz
eQTL-tools.imputed.SNP.anno,snpspos.chr2.txt.gz,snpspos.chr8.txt.gz,snpspos.chr7.txt.gz,snpspos.chr20.txt.gz,snpspos.chr14.txt.gz,snpspos.chr12.txt.gz,snpspos.chr19.txt.gz,snpspos.chr5.txt.gz,snpspos.chr4.txt.gz,snpspos.chr22.txt.gz,snpspos.chr21.txt.gz,snpspos.chr13.txt.gz,snpspos.chr1.txt.gz,snpspos.chr17.txt.gz,snpspos.chr10.txt.gz,snpspos.chr6.txt.gz,snpspos.chr3.txt.gz,snpspos.chr11.txt.gz,snpspos.chr16.txt.gz,snpspos.chr15.txt.gz,snpspos.chr9.txt.gz,snpspos.chr18.txt.gz
snpspos.chr2.txt.gz
snpspos.chr8.txt.gz
snpspos.chr7.txt.gz
snpspos.chr20.txt.gz
snpspos.chr14.txt.gz
snpspos.chr12.txt.gz
snpspos.chr19.txt.gz
snpspos.chr5.txt.gz
snpspos.chr4.txt.gz
snpspos.chr22.txt.gz
snpspos.chr21.txt.gz
snpspos.chr13.txt.gz
snpspos.chr1.txt.gz
snpspos.chr17.txt.gz
snpspos.chr10.txt.gz
snpspos.chr6.txt.gz
snpspos.chr3.txt.gz
snpspos.chr11.txt.gz
snpspos.chr16.txt.gz
snpspos.chr15.txt.gz
snpspos.chr9.txt.gz
snpspos.chr18.txt.gz
adj.gex,obs
obs,ucsc.10PC.adj.txt
ucsc.10PC.adj.txt
code,eqtl.tools-0.0.28,eqtl.tools-0.0.28.tar.gz,step.2.merge.peaks.pl,step.3.fdr.pl,step.1.1.pickup.sub.eqtl-lm-peaks.pl,step.4.cut.peak.pl
eqtl.tools-0.0.28.tar.gz
step.2.merge.peaks.pl
step.3.fdr.pl
step.1.1.pickup.sub.eqtl-lm-peaks.pl
step.4.cut.peak.pl
eqtl.tools-0.0.28,examples,test,COPYING,generate-example-data,kruskal,VERSION,INSTALL,table-subset,split-rows,Makefile,lm-sex,eqtl-sex-peaks,lm-cis,lm-suff,lm-fdr,lm-sort,find-peaks,eqtl-lm-peaks,cov_pairwise.c
COPYING
generate-example-data
kruskal
VERSION
INSTALL
table-subset
split-rows
Makefile
lm-sex
eqtl-sex-peaks
lm-cis
lm-suff
lm-fdr
lm-sort
find-peaks
eqtl-lm-peaks
cov_pairwise.c
examples,README
README
test,peaksTestInputAnnotation.tab,peaksTestInputData.tab,X.small.tab,X.ann,femalesIDs,Y.small.tab,Y.ann,malesIDs,Y.tab,X.tab
peaksTestInputAnnotation.tab
peaksTestInputData.tab
X.small.tab
X.ann
femalesIDs
Y.small.tab
Y.ann
malesIDs
Y.tab
X.tab
input dataset,Ucsc.annotation.hg19.txt
Ucsc.annotation.hg19.txt
Macrophage,NCKAP1L.R,TNFAIP3_code.R,New_group_May_11_2015.R,GPR65.R,Janssen_R_code_T17_T26.R,ReadMeForPhnotypeCorrelation.R,KD_gene_expression.Rdata,Venn.R,FRP1_code_updated.R,Macrophage_total_code.R,Biopsy.R,LAPTM5.R,example.R,MAFB_code_updated.R,GBP5_code.R,DOK3.R,GBP5.R,LAPTM5_code_updated.R,GPMS3.R,NCKAP1L_code.R,DOK3_code_updated.R,FPR1.R,Total_R.R,GPR65_code.R,R_key.R,NewR.R,Macrophage_0419_2015.R,SLAMF1_code_updated.R,AIF1_code.R,R04262015updated.R,DOCK3.R,workingCode.R,Checking_Code.R,MAFB_code.R,MAFB.R,JanssenKO_1.R,Mapping_aa.R,GPSM3_code_updated.R,TNFAIP3_code_updated.R,GBP5_code_updated.R,TNFAIP3.R,SLAMF1.R,summarySE.R,GPR65_code_updated.R,AIF1_code_updated.R,AIF1.R,LAPTM5_code.R,GPSM3_code.R,Correlation_code.R,New_R_code_May_8_2015.R,NCKAP1L_code_updated.R,DOK3_code.R,SLAMF1_code.R,Blood_Correlation2.R,Summary.R,R04262015.R,FPR1_code.R
NCKAP1L.R
TNFAIP3_code.R
New_group_May_11_2015.R
GPR65.R
Janssen_R_code_T17_T26.R
ReadMeForPhnotypeCorrelation.R
KD_gene_expression.Rdata
Venn.R
FRP1_code_updated.R
Macrophage_total_code.R
Biopsy.R
LAPTM5.R
example.R
MAFB_code_updated.R
GBP5_code.R
DOK3.R
GBP5.R
LAPTM5_code_updated.R
GPMS3.R
NCKAP1L_code.R
DOK3_code_updated.R
FPR1.R
Total_R.R
GPR65_code.R
R_key.R
NewR.R
Macrophage_0419_2015.R
SLAMF1_code_updated.R
AIF1_code.R
R04262015updated.R
DOCK3.R
workingCode.R
Checking_Code.R
MAFB_code.R
MAFB.R
JanssenKO_1.R
Mapping_aa.R
GPSM3_code_updated.R
TNFAIP3_code_updated.R
GBP5_code_updated.R
TNFAIP3.R
SLAMF1.R
summarySE.R
GPR65_code_updated.R
AIF1_code_updated.R
AIF1.R
LAPTM5_code.R
GPSM3_code.R
Correlation_code.R
New_R_code_May_8_2015.R
NCKAP1L_code_updated.R
DOK3_code.R
SLAMF1_code.R
Blood_Correlation2.R
Summary.R
R04262015.R
FPR1_code.R
GWASmapandIAMKDG,KDG pipeline in steps,GWASmapandenrich
KDG pipeline in steps,step 3 (project CIC IBD networks derived from core IAM onto intestinal BNs to identify key drivers).R,step 4.2 (computing overlaps between the KDG KO signatures and mac RNAi KD signatures and the mac specific cell signatures).R,step 4.4 (identify genes in the IBD networks that are least likely to be KDGs).R,step 4 (final ranking).R,step 5 (form the macrophage component of the IBD network).R,step 4.3 (compute mean rank per trait across IBD networks).R,step 1 generate core IAM module.R,step 4.1 (modifying core IAM based on final ranking to recompute starting with step 2).R,step 1b (project IBD signatures onto coexpression networks to assess enrichments of tagged modules).R,step 2 (project core -- combo -- IAM module onto intestinal BNs to get IBD CIC networks).R
step 3 (project CIC IBD networks derived from core IAM onto intestinal BNs to identify key drivers).R
step 4.2 (computing overlaps between the KDG KO signatures and mac RNAi KD signatures and the mac specific cell signatures).R
step 4.4 (identify genes in the IBD networks that are least likely to be KDGs).R
step 4 (final ranking).R
step 5 (form the macrophage component of the IBD network).R
step 4.3 (compute mean rank per trait across IBD networks).R
step 1 generate core IAM module.R
step 4.1 (modifying core IAM based on final ranking to recompute starting with step 2).R
step 1b (project IBD signatures onto coexpression networks to assess enrichments of tagged modules).R
step 2 (project core -- combo -- IAM module onto intestinal BNs to get IBD CIC networks).R
GWASmapandenrich,Assemble CRE and GWAS sets of interest and generate overlaps (CD4 T Cell Set).R,Assemble CRE and GWAS sets of interest and generate overlaps (Myeloid Set).R,Assemble CRE and GWAS sets of interest and generate overlaps (Digestive Set).R,CD4Generate overlap between cres-gwas overlaps and eqtl genes.R,NKcellsgenerate overlap between cres-gwas overlaps and eqtl genes.R,myeloid generate overlap between cres-gwas overlaps and eqtl genes.R,generate overlap between cres-gwas overlaps and eqtl genes.Bcell.R,link eqtl and gwas snps to ibd genes (1).R,CD8Tcell.generate overlap between cres-gwas overlaps and eqtl genes.R,Assemble CRE and GWAS sets of interest and generate overlaps (CD8 T Cell Set).R,Assemble CRE and GWAS sets of interest and generate overlaps NK Cell Set).R,Assemble CRE and GWAS sets of interest and generate overlaps (B Cell Set).R,Digestive-Assemble CRE and GWAS sets of interest and generate overlaps (Digestive Set).R
Assemble CRE and GWAS sets of interest and generate overlaps (CD4 T Cell Set).R
Assemble CRE and GWAS sets of interest and generate overlaps (Myeloid Set).R
Assemble CRE and GWAS sets of interest and generate overlaps (Digestive Set).R
CD4Generate overlap between cres-gwas overlaps and eqtl genes.R
NKcellsgenerate overlap between cres-gwas overlaps and eqtl genes.R
myeloid generate overlap between cres-gwas overlaps and eqtl genes.R
generate overlap between cres-gwas overlaps and eqtl genes.Bcell.R
link eqtl and gwas snps to ibd genes (1).R
CD8Tcell.generate overlap between cres-gwas overlaps and eqtl genes.R
Assemble CRE and GWAS sets of interest and generate overlaps (CD8 T Cell Set).R
Assemble CRE and GWAS sets of interest and generate overlaps NK Cell Set).R
Assemble CRE and GWAS sets of interest and generate overlaps (B Cell Set).R
Digestive-Assemble CRE and GWAS sets of interest and generate overlaps (Digestive Set).R
CREenrich,CES.R.txt,db.Rdata,.Rhistory,CRE.tsv
CES.R.txt
db.Rdata
.Rhistory
CRE.tsv
TF,main_TFA.R,Run_InferTFA_Public.R,GetOptimalWindowandActivity_Core_Public.R
main_TFA.R
Run_InferTFA_Public.R
GetOptimalWindowandActivity_Core_Public.R
analysis
Network,co-expression network,codeforenrichmenttable.R
codeforenrichmenttable.R
co-expression network,RUN_KDA.R,Curate_Signature.R,DEG.curated.RData,R_functions.R
RUN_KDA.R
Curate_Signature.R
DEG.curated.RData
R_functions.R