Files in MSKCC-Epi-Bio/gnomeR

Wrangle and analyze IMPACT and TCGA mutation data

.github/pull_request_template.R CODE_OF_CONDUCT.md LICENSE.md NEWS.md R/add-pathways.R R/annotate-panels.R R/create-gene-binary.R R/data.R R/gnomeR-package.R R/gnomer-color-palette.R R/pivot-cna.R R/plotting-functions.R R/reexport.R R/reformat_fusion.R R/resolve-gene-aliases.R R/subset-by-frequency.R R/subset-by-panel.R R/summarize-by-gene.R R/summarize-by-patient.R R/tbl_genomic.R R/utils-exported-helpers.R R/utils-gene-binary.R R/utils.R README.Rmd README.md data-raw/alias-table.R data-raw/api-data-example.R data-raw/clin_collab_df.R data-raw/consequence_map.R data-raw/data_schema.R data-raw/gene_panels.R data-raw/genie_NCCL_sample.R data-raw/pathways.R data-raw/sv_long.R data-raw/wide-cna-example.R inst/seg-stuff/facets.R inst/seg-stuff/mod-CNregions.R inst/seg-stuff/oncoprint.R man/add_pathways.Rd man/annotate_any_panel.Rd man/annotate_specific_panel.Rd man/clin_collab_df.Rd man/cna.Rd man/cna_wide.Rd man/consequence_map.Rd man/create_gene_binary.Rd man/dot-abort_if_not_numeric.Rd man/dot-check_for_fus_in_mut.Rd man/dot-check_for_silent.Rd man/dot-check_required_cols.Rd man/dot-clean_and_check_cols.Rd man/dot-cna_gene_binary.Rd man/dot-filter_to_sample_list.Rd man/dot-fusions_gene_binary.Rd man/dot-infer_mutation_status.Rd man/dot-infer_variant_type.Rd man/dot-mutations_gene_binary.Rd man/dot-paste_endings.Rd man/dot-process_binary.Rd man/dot-sum_alts_in_pathway.Rd man/extract_patient_id.Rd man/gene_panels.Rd man/genie_alias_table.Rd man/genie_cna.Rd man/genie_fusion.Rd man/genie_mut.Rd man/ggcomut.Rd man/gggenecor.Rd man/ggsamplevar.Rd man/ggtopgenes.Rd man/ggvarclass.Rd man/ggvartype.Rd man/gnomeR-package.Rd man/gnomer_colors.Rd man/gnomer_palette.Rd man/gnomer_palettes.Rd man/impact_alias_table.Rd man/mutation_viz.Rd man/mutations.Rd man/names_df.Rd man/pathways.Rd man/pivot_cna_longer.Rd man/pivot_cna_wider.Rd man/recode_alias.Rd man/recode_cna.Rd man/reexports.Rd man/reformat_fusion.Rd man/rename_columns.Rd man/reset_gnomer_palette.Rd man/resolve_alias.Rd man/seg.Rd man/set_gnomer_palette.Rd man/specify_impact_panels.Rd man/subset_by_frequency.Rd man/subset_by_panel.Rd man/summarize_by_gene.Rd man/summarize_by_patient.Rd man/sv.Rd man/sv_long.Rd man/tbl_genomic.Rd man/which_impact_panel.Rd tests/spelling.R tests/testthat.R tests/testthat/Rplots.pdf tests/testthat/test-add_pathways.R tests/testthat/test-binary-matrix.R tests/testthat/test-facets.R tests/testthat/test-genomic_tbl.R tests/testthat/test-pivot-cna.R tests/testthat/test-plots.R tests/testthat/test-process-binary.R tests/testthat/test-recode-alias.R tests/testthat/test-recode_cna_alterations.R tests/testthat/test-recoding_cna.R tests/testthat/test-reformat_fusion.R tests/testthat/test-rename_columns.R tests/testthat/test-sanitize.R tests/testthat/test-specify-panel.R tests/testthat/test-subset_by_freq.R tests/testthat/test-subset_by_panel.R tests/testthat/test-summarize-by-gene.R tests/testthat/test-summarize-by-patient.R tests/testthat/test-utils.R tests/testthat/test-which_panel.R tests/testthat/tests-archive/test_gen-summary.R tests/testthat/tests-archive/test_maf-summary.R tests/testthat/tests-archive/test_make-bin-mat.R tests/testthat/tests-archive/test_make-oncoprint-data.R tests/testthat/tests-archive/test_make-oncoprint.R tests/testthat/tests-archive/test_uni-cox.R vignettes/data-processing-vignette.Rmd