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50.permute_databases.sh
50.permute_databases.sh
 
 
50.permute_databases_pfocr.sh
50.permute_databases_pfocr.sh
 
 
Arch4_Installation_GEO_retrieval_title_parsing.R
Arch4_Installation_GEO_retrieval_title_parsing.R
 
 
Arch4_Installation_GEO_retrieval_title_parsing_v7.2.R
Arch4_Installation_GEO_retrieval_title_parsing_v7.2.R
 
 
Comp.adjP_permutation_GSE107868.jpeg
Comp.adjP_permutation_GSE107868.jpeg
 
 
Comp.adjP_permutation_GSE139061.jpeg
Comp.adjP_permutation_GSE139061.jpeg
 
 
Dockerfile
Dockerfile
 
 
GSEABenchmark_analyses.R
GSEABenchmark_analyses.R
 
 
GSEABenchmarkeR_rSEA.R
GSEABenchmarkeR_rSEA.R
 
 
GSEABenchmarkeR_rSEA_vs_ORA.pdf
GSEABenchmarkeR_rSEA_vs_ORA.pdf
 
 
GSE_human_568sets.txt
GSE_human_568sets.txt
 
 
GSE_index_162_100_perm_result_only_pfocr.rds
GSE_index_162_100_perm_result_only_pfocr.rds
 
 
GSE_keyword_description_human.txt
GSE_keyword_description_human.txt
 
 
GSE_toDiscuss
GSE_toDiscuss
 
 
GSE_toModifiy
GSE_toModifiy
 
 
Hair Follicle.R
Hair Follicle.R
 
 
PCA_GSE107868_permSet1.jpeg
PCA_GSE107868_permSet1.jpeg
 
 
PCA_GSE139061_permSet2.jpeg
PCA_GSE139061_permSet2.jpeg
 
 
Parsing_result_version6
Parsing_result_version6
 
 
Pericardium.R
Pericardium.R
 
 
Pfocr Pathway Analyses P14.png
Pfocr Pathway Analyses P14.png
 
 
PlotDistributionsOfTDPs.R
PlotDistributionsOfTDPs.R
 
 
PlotDistributionsOfTDPs_AUC_July_2021_GSEA.R
PlotDistributionsOfTDPs_AUC_July_2021_GSEA.R
 
 
PlotDistributionsOfTDPs_AUC_July_2021_ORA.R
PlotDistributionsOfTDPs_AUC_July_2021_ORA.R
 
 
PlotDistributionsOfTDPs_AUC_July_2021_TCGA_GSEA_SAMPLE_PERM.R
PlotDistributionsOfTDPs_AUC_July_2021_TCGA_GSEA_SAMPLE_PERM.R
 
 
PlotDistributionsOfTDPs_AUC_July_2021_TCGA_PADOG.R
PlotDistributionsOfTDPs_AUC_July_2021_TCGA_PADOG.R
 
 
PlotDistributionsOfTDPs_AUC_July_2021_TCGA_RSEA.R
PlotDistributionsOfTDPs_AUC_July_2021_TCGA_RSEA.R
 
 
PlotDistributionsOfTDPs_AUC_July_2021_TCGA_SAFE.R
PlotDistributionsOfTDPs_AUC_July_2021_TCGA_SAFE.R
 
 
PlotDistributionsOfTDPs_AUC_May_2021.R
PlotDistributionsOfTDPs_AUC_May_2021.R
 
 
PlotDistributionsOfTDPs_AUC_Sept_2021_TCGA_AllMethods.R
PlotDistributionsOfTDPs_AUC_Sept_2021_TCGA_AllMethods.R
 
 
PlotDistributionsOfTDPs_AUC_Sept_2021_rsea_sc.R
PlotDistributionsOfTDPs_AUC_Sept_2021_rsea_sc.R
 
 
PlotDistributionsOfTDPs_May_2021.R
PlotDistributionsOfTDPs_May_2021.R
 
 
README.md
README.md
 
 
ROC_curve.R
ROC_curve.R
 
 
SC.adjP_permutation_GSE107868.jpeg
SC.adjP_permutation_GSE107868.jpeg
 
 
SC.adjP_permutation_GSE139061.jpeg
SC.adjP_permutation_GSE139061.jpeg
 
 
Spinal Cord.R
Spinal Cord.R
 
 
compare_methods.R
compare_methods.R
 
 
compare_methods_GEO_data_sets.R
compare_methods_GEO_data_sets.R
 
 
cur-pf-terms.RDS
cur-pf-terms.RDS
 
 
cur-wp-terms.RDS
cur-wp-terms.RDS
 
 
disease-sets.R
disease-sets.R
 
 
disease-terms-intersect.csv
disease-terms-intersect.csv
 
 
disease-terms-pfocr.csv
disease-terms-pfocr.csv
 
 
disease-terms-union.csv
disease-terms-union.csv
 
 
disease-terms-wp.csv
disease-terms-wp.csv
 
 
exact_permutation_significant_gene_hist_set1.jpeg
exact_permutation_significant_gene_hist_set1.jpeg
 
 
exact_permutation_significant_gene_hist_set2.jpeg
exact_permutation_significant_gene_hist_set2.jpeg
 
 
generate_databases_from_msigdb.R
generate_databases_from_msigdb.R
 
 
get_genome_wide_tdp_tcga_data.R
get_genome_wide_tdp_tcga_data.R
 
 
gmt-pfocr-overlaps.RDS
gmt-pfocr-overlaps.RDS
 
 
gmt-wp-overlaps.RDS
gmt-wp-overlaps.RDS
 
 
groupC_com_15.jpeg
groupC_com_15.jpeg
 
 
groupC_hist_comb_small10.jpeg
groupC_hist_comb_small10.jpeg
 
 
groupC_hist_small10.jpeg
groupC_hist_small10.jpeg
 
 
group_max_sampleC_hist15.jpeg
group_max_sampleC_hist15.jpeg
 
 
groups_filtered_merged.RData
groups_filtered_merged.RData
 
 
hist_number_sig_genes_human.jpeg
hist_number_sig_genes_human.jpeg
 
 
human_gse_gene_count.txt
human_gse_gene_count.txt
 
 
human_knockout_go.txt
human_knockout_go.txt
 
 
human_knockout_go_April2021version.txt
human_knockout_go_April2021version.txt
 
 
human_knockout_pfocr.txt
human_knockout_pfocr.txt
 
 
human_knockout_pfocr_3sets_April2021version.txt
human_knockout_pfocr_3sets_April2021version.txt
 
 
human_knockout_pfocr_April2021version.txt
human_knockout_pfocr_April2021version.txt
 
 
human_knockout_wp.txt
human_knockout_wp.txt
 
 
human_knockout_wp_April2021version.txt
human_knockout_wp_April2021version.txt
 
 
make_rsea_input.R
make_rsea_input.R
 
 
method.log
method.log
 
 
ora_permutation_GSE107868.jpeg
ora_permutation_GSE107868.jpeg
 
 
ora_permutation_GSE139061.jpeg
ora_permutation_GSE139061.jpeg
 
 
parsing_v7.2.RData
parsing_v7.2.RData
 
 
parsing_v7.2_results7_noHistone_1comparison_2groups.RData
parsing_v7.2_results7_noHistone_1comparison_2groups.RData
 
 
parsing_v7_failures
parsing_v7_failures
 
 
perform_fishers_test.R
perform_fishers_test.R
 
 
permutation_significant_gene_hist_set1.jpeg
permutation_significant_gene_hist_set1.jpeg
 
 
permutation_significant_gene_hist_set2.jpeg
permutation_significant_gene_hist_set2.jpeg
 
 
permute_databases.sh
permute_databases.sh
 
 
permuted_gene_sets.R
permuted_gene_sets.R
 
 
permuted_gene_sets_gsea.R
permuted_gene_sets_gsea.R
 
 
permuted_gene_sets_ora.R
permuted_gene_sets_ora.R
 
 
permuted_gene_sets_pfocr.R
permuted_gene_sets_pfocr.R
 
 
permuted_gene_sets_rSEA_SCadjP.R
permuted_gene_sets_rSEA_SCadjP.R
 
 
permuted_gene_sets_rSEA_SCadjP_database.R
permuted_gene_sets_rSEA_SCadjP_database.R
 
 
permuted_gene_sets_tcga_gsea.R
permuted_gene_sets_tcga_gsea.R
 
 
permuted_gene_sets_tcga_gsea_effect_size_fixed_no_pathways.R
permuted_gene_sets_tcga_gsea_effect_size_fixed_no_pathways.R
 
 
permuted_gene_sets_tcga_gsea_test_parallel_comp.R
permuted_gene_sets_tcga_gsea_test_parallel_comp.R
 
 
permuted_gene_sets_tcga_padog.R
permuted_gene_sets_tcga_padog.R
 
 
permuted_gene_sets_tcga_padog_effect_size_fixed_no_pathways.R
permuted_gene_sets_tcga_padog_effect_size_fixed_no_pathways.R
 
 
permuted_gene_sets_tcga_rsea.R
permuted_gene_sets_tcga_rsea.R
 
 
permuted_gene_sets_tcga_rsea_effect_size_fixed_no_pathways.R
permuted_gene_sets_tcga_rsea_effect_size_fixed_no_pathways.R
 
 
permuted_gene_sets_tcga_rsea_sc.R
permuted_gene_sets_tcga_rsea_sc.R
 
 
permuted_gene_sets_tcga_rsea_sc_effect_size_fixed_no_pathways.R
permuted_gene_sets_tcga_rsea_sc_effect_size_fixed_no_pathways.R
 
 
permuted_gene_sets_tcga_safe.R
permuted_gene_sets_tcga_safe.R
 
 
permuted_gene_sets_tcga_safe_effect_size_fixed_no_pathways.R
permuted_gene_sets_tcga_safe_effect_size_fixed_no_pathways.R
 
 
permuted_gene_sets_v2.R
permuted_gene_sets_v2.R
 
 
permuted_set1_signiciant_rSEA_pathway_jaccard.jpeg
permuted_set1_signiciant_rSEA_pathway_jaccard.jpeg
 
 
permuted_set2_signiciant_rSEA_pathway_jaccard.jpeg
permuted_set2_signiciant_rSEA_pathway_jaccard.jpeg
 
 
rSEA_significant_pathway_count_human.jpeg
rSEA_significant_pathway_count_human.jpeg
 
 
simulateData4FishersExactTest.R
simulateData4FishersExactTest.R
 
 
target-datasets.RDS
target-datasets.RDS
 
 

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PFOCRInPathwayAnalyses

  1. I downloaded all the human data from the ARCHS4 database here. Beware! this is BIG file (7GB).
  2. For pathway analyses we could start working with the rSEA package.

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