Files in GeneAccord

Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

README.md

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

inst/extdata/clonal_genotypes/cloe_seed30/84.csv

inst/extdata/clonal_genotypes/cloe_seed30/18.csv

inst/extdata/clonal_genotypes/cloe_seed30/52.csv

inst/extdata/clonal_genotypes/cloe_seed30/60.csv

inst/extdata/clonal_genotypes/cloe_seed30/09.csv

inst/extdata/clonal_genotypes/cloe_seed30/47.csv

inst/extdata/clonal_genotypes/cloe_seed30/42.csv

inst/extdata/clonal_genotypes/cloe_seed30/79.csv

inst/extdata/clonal_genotypes/cloe_seed30/22.csv

inst/extdata/clonal_genotypes/cloe_seed30/61.csv

inst/extdata/clonal_genotypes/cloe_seed30/35.csv

inst/extdata/clonal_genotypes/cloe_seed30/46.csv

inst/extdata/clonal_genotypes/cloe_seed30/75.csv

inst/extdata/clonal_genotypes/cloe_seed30/73.csv

inst/extdata/clonal_genotypes/cloe_seed30/48.csv

inst/extdata/clonal_genotypes/cloe_seed30/76.csv

inst/extdata/clonal_genotypes/cloe_seed30/26.csv

inst/extdata/clonal_genotypes/cloe_seed30/08.csv

inst/extdata/clonal_genotypes/cloe_seed30/02.csv

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inst/extdata/clonal_genotypes/cloe_seed30/62.csv

inst/extdata/clonal_genotypes/cloe_seed30/25.csv

inst/extdata/clonal_genotypes/cloe_seed30/41.csv

inst/extdata/clonal_genotypes/cloe_seed30/13.csv

inst/extdata/clonal_genotypes/cloe_seed30/82.csv

inst/extdata/clonal_genotypes/cloe_seed30/89.csv

inst/extdata/clonal_genotypes/cloe_seed30/12.csv

inst/extdata/clonal_genotypes/cloe_seed30/70.csv

inst/extdata/clonal_genotypes/cloe_seed30/45.csv

inst/extdata/clonal_genotypes/cloe_seed30/56.csv

inst/extdata/clonal_genotypes/cloe_seed30/21.csv

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inst/extdata/clonal_genotypes/cloe_seed30/33.csv

inst/extdata/clonal_genotypes/cloe_seed30/16.csv

inst/extdata/clonal_genotypes/cloe_seed30/59.csv

inst/extdata/clonal_genotypes/cloe_seed30/85.csv

inst/extdata/clonal_genotypes/cloe_seed30/54.csv

inst/extdata/clonal_genotypes/cloe_seed30/69.csv

inst/extdata/clonal_genotypes/cloe_seed30/78.csv

inst/extdata/clonal_genotypes/cloe_seed30/50.csv

inst/extdata/clonal_genotypes/cloe_seed30/38.csv

inst/extdata/clonal_genotypes/cloe_seed30/81.csv

inst/extdata/clonal_genotypes/cloe_seed30/15.csv

inst/extdata/clonal_genotypes/cloe_seed30/88.csv

inst/extdata/clonal_genotypes/cloe_seed30/29.csv

inst/extdata/clonal_genotypes/cloe_seed30/68.csv

inst/extdata/clonal_genotypes/cloe_seed30/71.csv

inst/extdata/clonal_genotypes/cloe_seed30/57.csv

inst/extdata/clonal_genotypes/cloe_seed30/83.csv

inst/extdata/clonal_genotypes/cloe_seed30/04.csv

inst/extdata/clonal_genotypes/cloe_seed30/19.csv

inst/extdata/clonal_genotypes/cloe_seed30/31.csv

inst/extdata/clonal_genotypes/cloe_seed30/01.csv

inst/extdata/clonal_genotypes/cloe_seed30/55.csv

inst/extdata/clonal_genotypes/cloe_seed30/86.csv

inst/extdata/clonal_genotypes/cloe_seed30/67.csv

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

inst/extdata/clonal_genotypes/cloe_seed30/14.csv

inst/extdata/clonal_genotypes/cloe_seed30/39.csv

inst/extdata/clonal_genotypes/cloe_seed30/27.csv

inst/extdata/clonal_genotypes/cloe_seed30/80.csv

inst/extdata/clonal_genotypes/cloe_seed90/17.csv

inst/extdata/clonal_genotypes/cloe_seed90/49.csv

inst/extdata/clonal_genotypes/cloe_seed90/05.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

inst/extdata/clonal_genotypes/cloe_seed90/26.csv

inst/extdata/clonal_genotypes/cloe_seed90/08.csv

inst/extdata/clonal_genotypes/cloe_seed90/02.csv

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

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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

inst/extdata/clonal_genotypes/cloe_seed55/20.csv

inst/extdata/clonal_genotypes/cloe_seed55/23.csv

inst/extdata/clonal_genotypes/cloe_seed55/30.csv

inst/extdata/clonal_genotypes/cloe_seed55/66.csv

inst/extdata/clonal_genotypes/cloe_seed55/07.csv

inst/extdata/clonal_genotypes/cloe_seed55/44.csv

inst/extdata/clonal_genotypes/cloe_seed55/40.csv

inst/extdata/clonal_genotypes/cloe_seed55/43.csv

inst/extdata/clonal_genotypes/cloe_seed55/63.csv

inst/extdata/clonal_genotypes/cloe_seed55/64.csv

inst/extdata/clonal_genotypes/cloe_seed55/10.csv

inst/extdata/clonal_genotypes/cloe_seed55/77.csv

inst/extdata/clonal_genotypes/cloe_seed55/06.csv

inst/extdata/clonal_genotypes/cloe_seed55/84.csv

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inst/extdata/clonal_genotypes/cloe_seed55/52.csv

inst/extdata/clonal_genotypes/cloe_seed55/60.csv

inst/extdata/clonal_genotypes/cloe_seed55/09.csv

inst/extdata/clonal_genotypes/cloe_seed55/47.csv

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inst/extdata/clonal_genotypes/cloe_seed55/79.csv

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inst/extdata/clonal_genotypes/cloe_seed55/61.csv

inst/extdata/clonal_genotypes/cloe_seed55/35.csv

inst/extdata/clonal_genotypes/cloe_seed55/46.csv

inst/extdata/clonal_genotypes/cloe_seed55/75.csv

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inst/extdata/clonal_genotypes/cloe_seed55/48.csv

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inst/extdata/clonal_genotypes/cloe_seed55/26.csv

inst/extdata/clonal_genotypes/cloe_seed55/08.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

inst/extdata/clonal_genotypes/cloe_seed55/13.csv

inst/extdata/clonal_genotypes/cloe_seed55/82.csv

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

inst/extdata/clonal_genotypes/cloe_seed55/56.csv

inst/extdata/clonal_genotypes/cloe_seed55/21.csv

inst/extdata/clonal_genotypes/cloe_seed55/28.csv

inst/extdata/clonal_genotypes/cloe_seed55/33.csv

inst/extdata/clonal_genotypes/cloe_seed55/16.csv

inst/extdata/clonal_genotypes/cloe_seed55/59.csv

inst/extdata/clonal_genotypes/cloe_seed55/85.csv

inst/extdata/clonal_genotypes/cloe_seed55/54.csv

inst/extdata/clonal_genotypes/cloe_seed55/69.csv

inst/extdata/clonal_genotypes/cloe_seed55/78.csv

inst/extdata/clonal_genotypes/cloe_seed55/50.csv

inst/extdata/clonal_genotypes/cloe_seed55/38.csv

inst/extdata/clonal_genotypes/cloe_seed55/81.csv

inst/extdata/clonal_genotypes/cloe_seed55/15.csv

inst/extdata/clonal_genotypes/cloe_seed55/88.csv

inst/extdata/clonal_genotypes/cloe_seed55/29.csv

inst/extdata/clonal_genotypes/cloe_seed55/68.csv

inst/extdata/clonal_genotypes/cloe_seed55/71.csv

inst/extdata/clonal_genotypes/cloe_seed55/57.csv

inst/extdata/clonal_genotypes/cloe_seed55/83.csv

inst/extdata/clonal_genotypes/cloe_seed55/04.csv

inst/extdata/clonal_genotypes/cloe_seed55/19.csv

inst/extdata/clonal_genotypes/cloe_seed55/31.csv

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inst/extdata/clonal_genotypes/cloe_seed55/55.csv

inst/extdata/clonal_genotypes/cloe_seed55/86.csv

inst/extdata/clonal_genotypes/cloe_seed55/67.csv

inst/extdata/clonal_genotypes/cloe_seed55/32.csv

inst/extdata/clonal_genotypes/cloe_seed55/36.csv

inst/extdata/clonal_genotypes/cloe_seed55/74.csv

inst/extdata/clonal_genotypes/cloe_seed55/37.csv

inst/extdata/clonal_genotypes/cloe_seed55/72.csv

inst/extdata/clonal_genotypes/cloe_seed55/11.csv

inst/extdata/clonal_genotypes/cloe_seed55/14.csv

inst/extdata/clonal_genotypes/cloe_seed55/39.csv

inst/extdata/clonal_genotypes/cloe_seed55/27.csv

inst/extdata/clonal_genotypes/cloe_seed55/80.csv

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inst/extdata/clonal_genotypes/cloe_seed85/49.csv

inst/extdata/clonal_genotypes/cloe_seed85/05.csv

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inst/extdata/clonal_genotypes/cloe_seed85/30.csv

inst/extdata/clonal_genotypes/cloe_seed85/66.csv

inst/extdata/clonal_genotypes/cloe_seed85/07.csv

inst/extdata/clonal_genotypes/cloe_seed85/44.csv

inst/extdata/clonal_genotypes/cloe_seed85/40.csv

inst/extdata/clonal_genotypes/cloe_seed85/43.csv

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inst/extdata/clonal_genotypes/cloe_seed85/64.csv

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inst/extdata/clonal_genotypes/cloe_seed10/70.csv

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inst/extdata/clonal_genotypes/cloe_seed10/78.csv

inst/extdata/clonal_genotypes/cloe_seed10/50.csv

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inst/extdata/clonal_genotypes/cloe_seed10/81.csv

inst/extdata/clonal_genotypes/cloe_seed10/15.csv

inst/extdata/clonal_genotypes/cloe_seed10/88.csv

inst/extdata/clonal_genotypes/cloe_seed10/29.csv

inst/extdata/clonal_genotypes/cloe_seed10/68.csv

inst/extdata/clonal_genotypes/cloe_seed10/71.csv

inst/extdata/clonal_genotypes/cloe_seed10/57.csv

inst/extdata/clonal_genotypes/cloe_seed10/83.csv

inst/extdata/clonal_genotypes/cloe_seed10/04.csv

inst/extdata/clonal_genotypes/cloe_seed10/19.csv

inst/extdata/clonal_genotypes/cloe_seed10/31.csv

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inst/extdata/clonal_genotypes/cloe_seed10/55.csv

inst/extdata/clonal_genotypes/cloe_seed10/86.csv

inst/extdata/clonal_genotypes/cloe_seed10/67.csv

inst/extdata/clonal_genotypes/cloe_seed10/32.csv

inst/extdata/clonal_genotypes/cloe_seed10/36.csv

inst/extdata/clonal_genotypes/cloe_seed10/74.csv

inst/extdata/clonal_genotypes/cloe_seed10/37.csv

inst/extdata/clonal_genotypes/cloe_seed10/72.csv

inst/extdata/clonal_genotypes/cloe_seed10/11.csv

inst/extdata/clonal_genotypes/cloe_seed10/14.csv

inst/extdata/clonal_genotypes/cloe_seed10/39.csv

inst/extdata/clonal_genotypes/cloe_seed10/27.csv

inst/extdata/clonal_genotypes/cloe_seed10/80.csv

GeneAccord documentation built on Nov. 8, 2020, 8:04 p.m.