Files in GeneAccord
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients
README.md
GeneAccord documentation built on Nov. 8, 2020, 8:04 p.m.
NAMESPACE
DESCRIPTION
LICENSE
build/vignette.rds
data/ensmusg_reactome_path_map.RData
data/list_of_num_trees_all_pats.RData
data/list_of_clon_excl_all_pats.RData
data/clone_tbl_all_pats_all_trees.RData
data/ecdf_list.RData
data/all_genes_tbl.RData
data/avg_rates_m.RData
data/ensg_reactome_path_map.RData
R/GeneAccord_main_functions.R
R/stats_functions.R
R/plot_functions.R
R/data_handling_functions.R
R/databases_handling_functions.R
R/sim_functions.R
R/data.R
vignettes/GeneAccord.Rmd
man/ecdf_lr_test_clon_excl_avg_rate.Rd
man/take_pairs_and_get_patients.Rd
man/is_diff_branch_ent_pair.Rd
man/get_hist_clon_excl.Rd
man/convert_ensembl_to_reactome_pw_tbl.Rd
man/hgnc_to_ensembl.Rd
man/write_res_pairs_to_disk.Rd
man/map_pairs_to_hgnc_symbols.Rd
man/compute_test_stat_avg_rate.Rd
man/plot_ecdf_test_stat.Rd
man/vis_pval_distr_num_pat.Rd
man/get_hist_clon_excl_this_pat_this_pair.Rd
man/ensg_reactome_path_map.Rd
man/create_tbl_ent_clones.Rd
man/generate_ecdf_test_stat.Rd
man/generate_test_stat_hist.Rd
man/ensembl_to_hgnc.Rd
man/ensmusg_reactome_path_map.Rd
man/all_genes_tbl.Rd
man/list_of_num_trees_all_pats.Rd
man/avg_rates_m.Rd
man/create_ensembl_gene_tbl_hg.Rd
man/heatmap_clones_gene_pat.Rd
man/merge_clones_identical_ents.Rd
man/pairs_in_patients_hist.Rd
man/get_rate_diff_branch_ent_pair.Rd
man/build_null_test_statistic.Rd
man/create_tbl_tree_collection.Rd
man/plot_rates_clon_excl.Rd
man/extract_num_clones_tbl.Rd
man/clone_tbl_all_pats_all_trees.Rd
man/compute_rates_clon_excl.Rd
man/list_of_clon_excl_all_pats.Rd
man/ensembl_to_reactome.Rd
man/ecdf_list.Rd
man/GeneAccord.Rd
tests/testthat.R
tests/testthat/test_data_handling_functions.R
tests/testthat/test_plot_functions.R
tests/testthat/test_GeneAccord_main_functions.R
tests/testthat/test_databases_handling_functions.R
tests/testthat/test_sim_functions.R
tests/testthat/test_stats_functions.R
inst/NEWS.Rd
inst/CITATION
inst/doc/GeneAccord.Rmd
inst/doc/GeneAccord.html
inst/doc/GeneAccord.R
inst/extdata/Cartoon_GeneAccordAlgorithm_Rpackage.png
inst/extdata/prepare_patient_data_all.R
inst/extdata/README
inst/extdata/clonal_genotypes/cloe_seed30/17.csv
inst/extdata/clonal_genotypes/cloe_seed30/49.csv
inst/extdata/clonal_genotypes/cloe_seed30/05.csv
inst/extdata/clonal_genotypes/cloe_seed30/20.csv
inst/extdata/clonal_genotypes/cloe_seed30/23.csv
inst/extdata/clonal_genotypes/cloe_seed30/30.csv
inst/extdata/clonal_genotypes/cloe_seed30/66.csv
inst/extdata/clonal_genotypes/cloe_seed30/07.csv
inst/extdata/clonal_genotypes/cloe_seed30/44.csv
inst/extdata/clonal_genotypes/cloe_seed30/40.csv
inst/extdata/clonal_genotypes/cloe_seed30/43.csv
inst/extdata/clonal_genotypes/cloe_seed30/63.csv
inst/extdata/clonal_genotypes/cloe_seed30/64.csv
inst/extdata/clonal_genotypes/cloe_seed30/10.csv
inst/extdata/clonal_genotypes/cloe_seed30/77.csv
inst/extdata/clonal_genotypes/cloe_seed30/06.csv
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inst/extdata/clonal_genotypes/cloe_seed30/60.csv
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inst/extdata/clonal_genotypes/cloe_seed30/47.csv
inst/extdata/clonal_genotypes/cloe_seed30/42.csv
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inst/extdata/clonal_genotypes/cloe_seed30/22.csv
inst/extdata/clonal_genotypes/cloe_seed30/61.csv
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inst/extdata/clonal_genotypes/cloe_seed30/41.csv
inst/extdata/clonal_genotypes/cloe_seed30/13.csv
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inst/extdata/clonal_genotypes/cloe_seed30/89.csv
inst/extdata/clonal_genotypes/cloe_seed30/12.csv
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inst/extdata/clonal_genotypes/cloe_seed30/45.csv
inst/extdata/clonal_genotypes/cloe_seed30/56.csv
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inst/extdata/clonal_genotypes/cloe_seed30/33.csv
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inst/extdata/clonal_genotypes/cloe_seed30/69.csv
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inst/extdata/clonal_genotypes/cloe_seed30/38.csv
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inst/extdata/clonal_genotypes/cloe_seed30/15.csv
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inst/extdata/clonal_genotypes/cloe_seed30/29.csv
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inst/extdata/clonal_genotypes/cloe_seed30/57.csv
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inst/extdata/clonal_genotypes/cloe_seed30/04.csv
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inst/extdata/clonal_genotypes/cloe_seed30/31.csv
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inst/extdata/clonal_genotypes/cloe_seed30/55.csv
inst/extdata/clonal_genotypes/cloe_seed30/86.csv
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inst/extdata/clonal_genotypes/cloe_seed30/32.csv
inst/extdata/clonal_genotypes/cloe_seed30/36.csv
inst/extdata/clonal_genotypes/cloe_seed30/74.csv
inst/extdata/clonal_genotypes/cloe_seed30/37.csv
inst/extdata/clonal_genotypes/cloe_seed30/72.csv
inst/extdata/clonal_genotypes/cloe_seed30/11.csv
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inst/extdata/clonal_genotypes/cloe_seed30/27.csv
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inst/extdata/clonal_genotypes/cloe_seed90/17.csv
inst/extdata/clonal_genotypes/cloe_seed90/49.csv
inst/extdata/clonal_genotypes/cloe_seed90/05.csv
inst/extdata/clonal_genotypes/cloe_seed90/20.csv
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inst/extdata/clonal_genotypes/cloe_seed90/30.csv
inst/extdata/clonal_genotypes/cloe_seed90/66.csv
inst/extdata/clonal_genotypes/cloe_seed90/07.csv
inst/extdata/clonal_genotypes/cloe_seed90/44.csv
inst/extdata/clonal_genotypes/cloe_seed90/40.csv
inst/extdata/clonal_genotypes/cloe_seed90/43.csv
inst/extdata/clonal_genotypes/cloe_seed90/63.csv
inst/extdata/clonal_genotypes/cloe_seed90/64.csv
inst/extdata/clonal_genotypes/cloe_seed90/10.csv
inst/extdata/clonal_genotypes/cloe_seed90/77.csv
inst/extdata/clonal_genotypes/cloe_seed90/06.csv
inst/extdata/clonal_genotypes/cloe_seed90/84.csv
inst/extdata/clonal_genotypes/cloe_seed90/18.csv
inst/extdata/clonal_genotypes/cloe_seed90/52.csv
inst/extdata/clonal_genotypes/cloe_seed90/60.csv
inst/extdata/clonal_genotypes/cloe_seed90/09.csv
inst/extdata/clonal_genotypes/cloe_seed90/47.csv
inst/extdata/clonal_genotypes/cloe_seed90/42.csv
inst/extdata/clonal_genotypes/cloe_seed90/79.csv
inst/extdata/clonal_genotypes/cloe_seed90/22.csv
inst/extdata/clonal_genotypes/cloe_seed90/61.csv
inst/extdata/clonal_genotypes/cloe_seed90/35.csv
inst/extdata/clonal_genotypes/cloe_seed90/46.csv
inst/extdata/clonal_genotypes/cloe_seed90/75.csv
inst/extdata/clonal_genotypes/cloe_seed90/73.csv
inst/extdata/clonal_genotypes/cloe_seed90/48.csv
inst/extdata/clonal_genotypes/cloe_seed90/76.csv
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inst/extdata/clonal_genotypes/cloe_seed90/24.csv
inst/extdata/clonal_genotypes/cloe_seed90/62.csv
inst/extdata/clonal_genotypes/cloe_seed90/25.csv
inst/extdata/clonal_genotypes/cloe_seed90/41.csv
inst/extdata/clonal_genotypes/cloe_seed90/13.csv
inst/extdata/clonal_genotypes/cloe_seed90/82.csv
inst/extdata/clonal_genotypes/cloe_seed90/89.csv
inst/extdata/clonal_genotypes/cloe_seed90/12.csv
inst/extdata/clonal_genotypes/cloe_seed90/70.csv
inst/extdata/clonal_genotypes/cloe_seed90/45.csv
inst/extdata/clonal_genotypes/cloe_seed90/56.csv
inst/extdata/clonal_genotypes/cloe_seed90/21.csv
inst/extdata/clonal_genotypes/cloe_seed90/28.csv
inst/extdata/clonal_genotypes/cloe_seed90/33.csv
inst/extdata/clonal_genotypes/cloe_seed90/16.csv
inst/extdata/clonal_genotypes/cloe_seed90/59.csv
inst/extdata/clonal_genotypes/cloe_seed90/85.csv
inst/extdata/clonal_genotypes/cloe_seed90/54.csv
inst/extdata/clonal_genotypes/cloe_seed90/69.csv
inst/extdata/clonal_genotypes/cloe_seed90/78.csv
inst/extdata/clonal_genotypes/cloe_seed90/50.csv
inst/extdata/clonal_genotypes/cloe_seed90/38.csv
inst/extdata/clonal_genotypes/cloe_seed90/81.csv
inst/extdata/clonal_genotypes/cloe_seed90/15.csv
inst/extdata/clonal_genotypes/cloe_seed90/88.csv
inst/extdata/clonal_genotypes/cloe_seed90/29.csv
inst/extdata/clonal_genotypes/cloe_seed90/68.csv
inst/extdata/clonal_genotypes/cloe_seed90/71.csv
inst/extdata/clonal_genotypes/cloe_seed90/57.csv
inst/extdata/clonal_genotypes/cloe_seed90/83.csv
inst/extdata/clonal_genotypes/cloe_seed90/04.csv
inst/extdata/clonal_genotypes/cloe_seed90/19.csv
inst/extdata/clonal_genotypes/cloe_seed90/31.csv
inst/extdata/clonal_genotypes/cloe_seed90/01.csv
inst/extdata/clonal_genotypes/cloe_seed90/55.csv
inst/extdata/clonal_genotypes/cloe_seed90/86.csv
inst/extdata/clonal_genotypes/cloe_seed90/67.csv
inst/extdata/clonal_genotypes/cloe_seed90/32.csv
inst/extdata/clonal_genotypes/cloe_seed90/36.csv
inst/extdata/clonal_genotypes/cloe_seed90/74.csv
inst/extdata/clonal_genotypes/cloe_seed90/37.csv
inst/extdata/clonal_genotypes/cloe_seed90/72.csv
inst/extdata/clonal_genotypes/cloe_seed90/11.csv
inst/extdata/clonal_genotypes/cloe_seed90/14.csv
inst/extdata/clonal_genotypes/cloe_seed90/39.csv
inst/extdata/clonal_genotypes/cloe_seed90/27.csv
inst/extdata/clonal_genotypes/cloe_seed90/80.csv
inst/extdata/clonal_genotypes/cloe_seed55/17.csv
inst/extdata/clonal_genotypes/cloe_seed55/49.csv
inst/extdata/clonal_genotypes/cloe_seed55/05.csv
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inst/extdata/clonal_genotypes/cloe_seed55/07.csv
inst/extdata/clonal_genotypes/cloe_seed55/44.csv
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inst/extdata/clonal_genotypes/cloe_seed55/62.csv
inst/extdata/clonal_genotypes/cloe_seed55/25.csv
inst/extdata/clonal_genotypes/cloe_seed55/41.csv
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inst/extdata/clonal_genotypes/cloe_seed55/89.csv
inst/extdata/clonal_genotypes/cloe_seed55/12.csv
inst/extdata/clonal_genotypes/cloe_seed55/70.csv
inst/extdata/clonal_genotypes/cloe_seed55/45.csv
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