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Copy pathDirectoryNodes_wPaths.csv
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PAPER_DATA,PAPER_DATA/Gene.expression.by.SNP.genotype,PAPER_DATA/IBD Networks,PAPER_DATA/IBD Datasets,PAPER_DATA/CERTIFI DNA,PAPER_DATA/Code
PAPER_DATA/Gene.expression.by.SNP.genotype,PAPER_DATA/Gene.expression.by.SNP.genotype/CERTIFI,PAPER_DATA/Gene.expression.by.SNP.genotype/MSH,PAPER_DATA/Gene.expression.by.SNP.genotype/RISK,PAPER_DATA/Gene.expression.by.SNP.genotype/IBD.GPS_SNP_HLA.subtypes_coefficients_with_risk_allele_frequencies.xlsx,PAPER_DATA/Gene.expression.by.SNP.genotype/score_density.png
PAPER_DATA/Gene.expression.by.SNP.genotype/IBD.GPS_SNP_HLA.subtypes_coefficients_with_risk_allele_frequencies.xlsx
PAPER_DATA/Gene.expression.by.SNP.genotype/score_density.png
PAPER_DATA/Gene.expression.by.SNP.genotype/CERTIFI,PAPER_DATA/Gene.expression.by.SNP.genotype/CERTIFI/genotype_EAF.xls,PAPER_DATA/Gene.expression.by.SNP.genotype/CERTIFI/stats.xls
PAPER_DATA/Gene.expression.by.SNP.genotype/CERTIFI/genotype_EAF.xls
PAPER_DATA/Gene.expression.by.SNP.genotype/CERTIFI/stats.xls
PAPER_DATA/Gene.expression.by.SNP.genotype/MSH,PAPER_DATA/Gene.expression.by.SNP.genotype/MSH/genotype_EAF.xls,PAPER_DATA/Gene.expression.by.SNP.genotype/MSH/stats.xls
PAPER_DATA/Gene.expression.by.SNP.genotype/MSH/genotype_EAF.xls
PAPER_DATA/Gene.expression.by.SNP.genotype/MSH/stats.xls
PAPER_DATA/Gene.expression.by.SNP.genotype/RISK,PAPER_DATA/Gene.expression.by.SNP.genotype/RISK/genotype_EAF.xls,PAPER_DATA/Gene.expression.by.SNP.genotype/RISK/stats.xls
PAPER_DATA/Gene.expression.by.SNP.genotype/RISK/genotype_EAF.xls
PAPER_DATA/Gene.expression.by.SNP.genotype/RISK/stats.xls
PAPER_DATA/IBD Networks,PAPER_DATA/IBD Networks/Co-expressionnetworks,PAPER_DATA/IBD Networks/Bayesiannetworks
PAPER_DATA/IBD Networks/Co-expressionnetworks,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment,PAPER_DATA/IBD Networks/Co-expressionnetworks/Release Modules,PAPER_DATA/IBD Networks/Co-expressionnetworks/MSigDB_Enrichment,PAPER_DATA/IBD Networks/Co-expressionnetworks/Ontology Analysis,PAPER_DATA/IBD Networks/Co-expressionnetworks/GO_TermEnrichment,PAPER_DATA/IBD Networks/Co-expressionnetworks/IBD_T26_expression_Module-Trait-Correlations
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_ileum_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_RISK-filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_colon_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_RISK-filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_ALL_MSH2_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_ALL_MSH2_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_T26-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_colon_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_ileum_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_T26-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_RISK-filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_ALL_MSH2_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_colon_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_ileum_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_T26-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_colon_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_ileum_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_ALL_MSH2_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_T26-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls,PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_RISK-filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_ileum_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_RISK-filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_colon_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_RISK-filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_ALL_MSH2_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_ALL_MSH2_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_T26-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_colon_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_ileum_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_T26-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_RISK-filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_ALL_MSH2_filtered-vs-abc-cell-gpl570-signatures-filtered_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_colon_filtered-vs-abc-tis-gpl570-signatures-filtered_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_ileum_filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_T26-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_colon_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_MSH2_ileum_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_ALL_MSH2_filtered-vs-abc-tis-gpl570-signatures-lowent_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_T26-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
PAPER_DATA/IBD Networks/Co-expressionnetworks/Celltype_Enrichment/intersect_RISK-filtered-vs-abc-cell-gpl570-signatures-lowent_pair-restricted.xls
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PAPER_DATA/Code/GWASmapandIAMKDG/KDG pipeline in steps/step 3 (project CIC IBD networks derived from core IAM onto intestinal BNs to identify key drivers).R
PAPER_DATA/Code/GWASmapandIAMKDG/KDG pipeline in steps/step 4.2 (computing overlaps between the KDG KO signatures and mac RNAi KD signatures and the mac specific cell signatures).R
PAPER_DATA/Code/GWASmapandIAMKDG/KDG pipeline in steps/step 4.4 (identify genes in the IBD networks that are least likely to be KDGs).R
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PAPER_DATA/Code/GWASmapandIAMKDG/KDG pipeline in steps/step 5 (form the macrophage component of the IBD network).R
PAPER_DATA/Code/GWASmapandIAMKDG/KDG pipeline in steps/step 4.3 (compute mean rank per trait across IBD networks).R
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PAPER_DATA/Code/GWASmapandIAMKDG/KDG pipeline in steps/step 4.1 (modifying core IAM based on final ranking to recompute starting with step 2).R
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PAPER_DATA/Code/GWASmapandIAMKDG/GWASmapandenrich/NKcellsgenerate overlap between cres-gwas overlaps and eqtl genes.R
PAPER_DATA/Code/GWASmapandIAMKDG/GWASmapandenrich/myeloid generate overlap between cres-gwas overlaps and eqtl genes.R
PAPER_DATA/Code/GWASmapandIAMKDG/GWASmapandenrich/generate overlap between cres-gwas overlaps and eqtl genes.Bcell.R
PAPER_DATA/Code/GWASmapandIAMKDG/GWASmapandenrich/link eqtl and gwas snps to ibd genes (1).R
PAPER_DATA/Code/GWASmapandIAMKDG/GWASmapandenrich/CD8Tcell.generate overlap between cres-gwas overlaps and eqtl genes.R
PAPER_DATA/Code/GWASmapandIAMKDG/GWASmapandenrich/Assemble CRE and GWAS sets of interest and generate overlaps (CD8 T Cell Set).R
PAPER_DATA/Code/GWASmapandIAMKDG/GWASmapandenrich/Assemble CRE and GWAS sets of interest and generate overlaps NK Cell Set).R
PAPER_DATA/Code/GWASmapandIAMKDG/GWASmapandenrich/Assemble CRE and GWAS sets of interest and generate overlaps (B Cell Set).R
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