Files in BaderLab/POPPATHR

Population-based pathway analysis of SNP-SNP coevolution

LICENSE.md R/SNP2gene.R R/SNPassocBPM.R R/SNPassocWPM.R R/calcFST.R R/getBiogrid.R R/plotEmap.R R/popPCA.R R/recodeFAM.R R/setupGSEArun.R R/writeEmapFile.R R/writePathFiles.R R/~old/R/LDstatsBPM.R R/~old/R/LDstatsWPM.R R/~old/R/SNP2gene.R R/~old/R/calcFST.R R/~old/R/forPub/bpmPathAnno_forPub.R R/~old/R/forPub/compareBiogrid.R R/~old/R/forPub/diffMaf_vs_fst.R R/~old/R/forPub/fix_gseaStat_forPub.R R/~old/R/forPub/fst_vs_pathway.R R/~old/R/forPub/genePropertyIntegration_forPub.R R/~old/R/forPub/genePropertyIntegration_forPub_v2.R R/~old/R/forPub/getBiogridQualifications_forPub.R R/~old/R/forPub/getEMclusters.R R/~old/R/forPub/getGeneProps.R R/~old/R/forPub/gwas_adaptiveTraits.R R/~old/R/forPub/prop4topGene.R R/~old/R/forPub/tableStats_forPub.R R/~old/R/getGeneProps.R R/~old/R/getPathStats.R R/~old/R/popPCA.R R/~old/R/post_plots/annotateSnps.R R/~old/R/post_plots/biogrid_genetic_ixns.R R/~old/R/post_plots/biogrid_sig_test.R R/~old/R/post_plots/bpm_network_cowplot.R R/~old/R/post_plots/bpm_pathway_freq_ceu_yri.R R/~old/R/post_plots/circle.R R/~old/R/post_plots/circos.R R/~old/R/post_plots/circos_other-pathway.R R/~old/R/post_plots/compare_deltamaf.R R/~old/R/post_plots/compositeLD.R R/~old/R/post_plots/crossref_selection_akey.R R/~old/R/post_plots/dbpshp_all_genes.R R/~old/R/post_plots/dbpshp_function_wordcloud.R R/~old/R/post_plots/density_pubPlot.R R/~old/R/post_plots/diff_fst_absDmaf.R R/~old/R/post_plots/dmaf_all_vs_gene-map_pnc_hm3.R R/~old/R/post_plots/dmaf_directional_abs_plot.R R/~old/R/post_plots/enrich_unenrich_gene_overlap_violin_venn.R R/~old/R/post_plots/eqtl_enriched.R R/~old/R/post_plots/fgsea_enrichment_plot.R R/~old/R/post_plots/fgsea_plots_resTest.R R/~old/R/post_plots/filterGmt.R R/~old/R/post_plots/fst_boxplot_em_groups_cowplot.R R/~old/R/post_plots/fst_boxplot_em_groups_cowplot_updated.R R/~old/R/post_plots/fst_boxplot_pathways_cowplot.R R/~old/R/post_plots/fst_pop_test.R R/~old/R/post_plots/fst_violin_compare_cowplot.R R/~old/R/post_plots/genos_pop_pathway_cowplot.R R/~old/R/post_plots/gsea-stat_all_pathways.R R/~old/R/post_plots/gsea-stat_corr_deltamaf_defs.R R/~old/R/post_plots/gsea-stat_per_pathway.R R/~old/R/post_plots/gsea-stat_pnc_subsample.R R/~old/R/post_plots/gsea_size_vs_es.R R/~old/R/post_plots/gsea_yri_lwk_replicate_cowplot.R R/~old/R/post_plots/ixn_heatmap_between_pathway.R R/~old/R/post_plots/ixn_heatmap_between_pathway_both_pops.R R/~old/R/post_plots/ixn_heatmap_within_pathway.R R/~old/R/post_plots/ixn_heatmap_within_pathway_both_pops.R R/~old/R/post_plots/justLDstats.R R/~old/R/post_plots/maf_plink-freq_case-control.R R/~old/R/post_plots/manhattan_plot.R R/~old/R/post_plots/numProteinCodeGenes.R R/~old/R/post_plots/orginal_pathway_size.R R/~old/R/post_plots/pca_fst_distribution_cowplot.R R/~old/R/post_plots/pca_maf_distribution_cowplot.R R/~old/R/post_plots/permdebug.R R/~old/R/post_plots/plot_gsea_stats.R R/~old/R/post_plots/power.R R/~old/R/post_plots/power_new_data.R R/~old/R/post_plots/readPathways.R R/~old/R/post_plots/sample_dist.R R/~old/R/post_plots/selected_qtl_nedelec.R R/~old/R/post_plots/super_pathway_plink.R R/~old/R/post_plots/world_pca_cowplot.R R/~old/R/post_plots/worldmap.R R/~old/R/recodeFAM.R R/~old/R/runPipeline.R R/~old/R/setupGSEArun.R R/~old/R/themePublication.R R/~old/README.md R/~old/dev/1_gsea/calcMAFdiff.R R/~old/dev/1_gsea/calculateMAFdiff_withinClusters.R R/~old/dev/1_gsea/getSnpLists.R R/~old/dev/1_gsea/getSnpLists_pops.R R/~old/dev/1_gsea/pathwayAnnoCORUM.R R/~old/dev/1_gsea/popPCA.R R/~old/dev/1_gsea/runGSEA.R R/~old/dev/1_gsea/runPathway.R R/~old/dev/1_gsea/setupGSEArun.R R/~old/dev/1_gsea/validation/removeTopGenesSNP2gene.R R/~old/dev/1_gsea/validation/writeTopGenes.R R/~old/dev/2_snpstats/calculateAssoc.R R/~old/dev/2_snpstats/calculateAssoc_pops.R R/~old/dev/2_snpstats/calculateAssoc_ssLD.R R/~old/dev/2_snpstats/calculateFst_plink.R R/~old/dev/2_snpstats/calculateR2_plink.R R/~old/dev/2_snpstats/quickPlots.R R/~old/dev/2_snpstats/runAssocStats.R R/~old/dev/3_funcisnp/formatFunciSnpInput.R R/~old/dev/3_funcisnp/moreFun.R R/~old/dev/3_funcisnp/postAnalysis.R R/~old/dev/3_funcisnp/scinet/FunciSNP_run2.R R/~old/dev/3_funcisnp/scinet/prepareBiofeature.R R/~old/dev/4_caviar/identifyCausalSnps.R R/~old/dev/5_annovar/annotateSnps.R R/~old/dev/5_annovar/runAnnoVar.R R/~old/dev/LDstats.R R/~old/dev/LDstats_pseudo.R R/~old/dev/LDstats_rand.R R/~old/dev/calcMAFdiff.R R/~old/dev/exampleRwrapper.R R/~old/dev/getPathStats_2.R R/~old/dev/makePseudoPaths.R R/~old/dev/pathPosSel.R R/~old/dev/runPipeline_pnc.R R/~old/gpc/LDstats.R R/~old/gpc/SNP2gene.R R/~old/gpc/calcMAFdiff.R R/~old/gpc/getSNPlists.R R/~old/gpc/popPCA.R R/~old/gpc/recodeFAM.R R/~old/gpc/setupGSEArun.R R/~old/pipeline.md README.md get_coevolution.R get_enrichment.R get_properties.R man/SNP2gene.Rd man/SNPassocBPM.Rd man/SNPassocWPM.Rd man/calcFST.Rd man/getBiogrid.Rd man/plotEmap.Rd man/popPCA.Rd man/recodeFAM.Rd man/setupGSEArun.Rd man/writeEmapFile.Rd man/writePathFiles.Rd tests/testthat.R