PhD-Project-2.4

Assessing dIfferential expression, dispersion, distribution analyses on TCGA tumour-normal RNA-seq datasets

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PhD-Project-2.4

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Name		Name	Last commit message	Last commit date
Latest commit History 17 Commits
DE_v_DD_figures_for_paper.R		DE_v_DD_figures_for_paper.R
DE_v_DD_figures_for_thesis.R		DE_v_DD_figures_for_thesis.R
GSEA_file_prep_and_removing_redundant_results.R		GSEA_file_prep_and_removing_redundant_results.R
README.md		README.md
TCGA_AUC.R		TCGA_AUC.R
TCGA_known_cancer_gene_plots_for_CCRU_talk.R		TCGA_known_cancer_gene_plots_for_CCRU_talk.R
TCGA_matched_pair_analysis.R		TCGA_matched_pair_analysis.R
TCGA_matched_pair_analysis_long_chain.R		TCGA_matched_pair_analysis_long_chain.R
TCGA_matched_pair_analysis_long_chain_20k.R		TCGA_matched_pair_analysis_long_chain_20k.R
TCGA_matched_pair_analysis_long_chain_combined_with_other_analyses.R		TCGA_matched_pair_analysis_long_chain_combined_with_other_analyses.R
TCGA_matched_pair_analysis_long_chain_combined_with_other_analyses_pathway_minus_known_genes.R		TCGA_matched_pair_analysis_long_chain_combined_with_other_analyses_pathway_minus_known_genes.R
TCGA_matched_pair_analysis_pathway_genes.R		TCGA_matched_pair_analysis_pathway_genes.R
TCGA_matched_pair_analysis_pathway_genes_without_known_genes.R		TCGA_matched_pair_analysis_pathway_genes_without_known_genes.R
TCGA_matched_pair_analysis_pathway_genes_without_known_genes_long_chain.R		TCGA_matched_pair_analysis_pathway_genes_without_known_genes_long_chain.R
TCGA_matched_pair_combined_analysis.R		TCGA_matched_pair_combined_analysis.R
TCGA_matched_pair_combined_analysis_all_chain_lengths.R		TCGA_matched_pair_combined_analysis_all_chain_lengths.R
analysing_GSEA_results.R		analysing_GSEA_results.R
check_for_consistent_processing_of_TCGA_datasets.R		check_for_consistent_processing_of_TCGA_datasets.R
exploring_recount_TCGA_data.R		exploring_recount_TCGA_data.R
exploring_recount_TCGA_data_and_getting_matched_pairs.R		exploring_recount_TCGA_data_and_getting_matched_pairs.R
exploring_tests_for_comparing_methods.R		exploring_tests_for_comparing_methods.R
get_KEGG_gene_lists.R		get_KEGG_gene_lists.R
investigating_GO_in_R_1.R		investigating_GO_in_R_1.R
investigating_GO_in_R_2.R		investigating_GO_in_R_2.R
investigating_GO_in_R_3.R		investigating_GO_in_R_3.R
investigating_TCGA_matched_pair_results.R		investigating_TCGA_matched_pair_results.R
make_cancer_gene_lists_with_ensembl_ids.R		make_cancer_gene_lists_with_ensembl_ids.R
make_cancer_pathway_gene_lists_without_known_genes.R		make_cancer_pathway_gene_lists_without_known_genes.R
make_matched_tumour_normal_TCGA_datasets.R		make_matched_tumour_normal_TCGA_datasets.R
prep_files_for_GSEA.R		prep_files_for_GSEA.R
processing_cancer_gene_lists.R		processing_cancer_gene_lists.R
processing_cancer_pathway_gene_lists.R		processing_cancer_pathway_gene_lists.R
rerun_TCGA_paired_data_with_HMs_to_get_disp_estimates.R		rerun_TCGA_paired_data_with_HMs_to_get_disp_estimates.R
run_TCGA_HMs_long_chains.R		run_TCGA_HMs_long_chains.R
run_all_methods_on_TCGA_paired_data.R		run_all_methods_on_TCGA_paired_data.R
test_GSEA_v_wilcoxon_rank_sum_for_enrichment_analysis.R		test_GSEA_v_wilcoxon_rank_sum_for_enrichment_analysis.R
test_concordance_between_exp_and_ln_HMs_using_TCGA_brca_data.R		test_concordance_between_exp_and_ln_HMs_using_TCGA_brca_data.R
test_ways_of_ranking_HM_results_to_remove_ties.R		test_ways_of_ranking_HM_results_to_remove_ties.R
working_out_GSEA_mean_v_disp_analysis.R		working_out_GSEA_mean_v_disp_analysis.R

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