Files in AxelitoMartin/gnomeR
Wrangle and analyze IMPACT and TCGA mutation data
.Rbuildignore
.github/.gitignore
.github/pull_request_template.R
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
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/tbl_genomic.R
R/utils-exported-helpers.R
R/utils-gene-binary.R
R/utils.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
codemeta.json
data-raw/accepted-column-names.csv
data-raw/alias-table.R
data-raw/api-data-example.R
data-raw/clin_collab_df.R
data-raw/clin_collab_df.Rdata
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/pathways.csv
data-raw/sv_long.R
data-raw/sv_long.csv
data-raw/wide-cna-example.R
data/clin_collab_df.rda
data/cna.rda
data/cna_wide.rda
data/consequence_map.rda
data/gene_panels.rda
data/genie_alias_table.rda
data/genie_cna.rda
data/genie_fusion.rda
data/genie_mut.rda
data/impact_alias_table.rda
data/mutations.rda
data/names_df.rda
data/pathways.rda
data/seg.rda
data/sv.rda
data/sv_long.rda
gnomeR.Rproj
inst/WORDLIST
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_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/figures/README-path_by_trt.png
man/figures/README-tbl_genomic_print.png
man/figures/README-unnamed-chunk-10-1.png
man/figures/README-unnamed-chunk-11-1.png
man/figures/README-unnamed-chunk-11-2.png
man/figures/README-unnamed-chunk-12-1.png
man/figures/README-unnamed-chunk-12-2.png
man/figures/README-unnamed-chunk-13-1.png
man/figures/README-unnamed-chunk-4-1.png
man/figures/README-unnamed-chunk-5-1.png
man/figures/README-unnamed-chunk-6-1.png
man/figures/README-unnamed-chunk-7-1.png
man/figures/README-unnamed-chunk-8-1.png
man/figures/README-unnamed-chunk-8-2.png
man/figures/README-unnamed-chunk-9-1.png
man/figures/README-unnamed-chunk-9-2.png
man/figures/gene_tbl_trt.png
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/figures/path_by_trt.png
man/figures/table_by_trt.png
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/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-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/.gitignore
vignettes/data-processing-vignette.Rmd
vignettes/genie-bpc-vignette.Rmd
vignettes/qa-impact-data.Rmd
