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/binary_matrix.R R/data.R R/facets.R R/gnomeR-package.R R/gnomer_color_palette.R R/mod-CNregions.R R/oncokb.R R/oncoprint.R R/plots.R R/summarize_by_gene.R R/tbl_genomic.R R/utils-pipe.R R/utils.R README.Rmd README.md
codecov.yml
data-raw/data_gene_panel_impact341.txt
data-raw/data_gene_panel_impact410.txt
data-raw/data_gene_panel_impact468.txt
data-raw/gene_panels.R data-raw/genie-gene-info.R data-raw/impact-gene-info.R data-raw/pathways.R
data-raw/pathways.csv
data/.DS_Store
data/clin.patients.rda
data/clin.sample.rda
data/cna.rda
data/curated_genes.rda
data/fusion.rda
data/gene_panels.rda
data/genie_gene_info.RData
data/genie_gene_info.rda
data/impact_gene_info.rda
data/mut.rda
data/panel_names.RData
data/panel_names.rda
data/pathways.rda
data/seg.rda
data/tcga_genes.rda
data/tcga_samples.rda
data/ti_341.rda
data/ti_410.rda
data/ti_468.rda
gnomeR.Rproj
inst/AnnotatorCore.py
inst/AnnotatorCore.pyc
inst/ClinicalDataAnnotator.py
inst/CnaAnnotator.py
inst/FusionAnnotator.py
inst/GenerateReadMe.py
inst/MafAnnotator.py
inst/OncoKBPlots.py
inst/README.md
inst/WORDLIST
inst/annotate_cna.py
inst/annotate_fusion.py
inst/annotate_maf.py
inst/curated_genes.txt
inst/example.sh
inst/example_clinical.txt
inst/example_cna.txt
inst/example_fusions.txt
inst/example_maf.txt
inst/requirements.txt
inst/test_AnnotatorCore.py
man/CNregions.mod.Rd man/add.perc.Rd man/add_pathways.Rd man/annotate_any_panel.Rd man/annotate_specific_panel.Rd man/check_cna_input.Rd man/check_fusion_input.Rd man/check_mutation_input.Rd man/clin.patients.Rd man/clin.sample.Rd man/cna.Rd man/create_gene_binary.Rd man/curated_genes.Rd man/dat_oncoprint.Rd man/dot-cna_gene_binary.Rd man/dot-fusions_gene_binary.Rd man/dot-mutations_gene_binary.Rd man/dot-sum_alts_in_pathway.Rd man/facets_dat.Rd man/facets_heatmap.Rd
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-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/fusion.Rd man/gene_panels.Rd man/genie_gene_info.Rd man/ggcomut.Rd man/gggenecor.Rd man/ggheatmap.Rd man/ggsamplevar.Rd man/ggsnvclass.Rd man/ggtopgenes.Rd man/ggvarclass.Rd man/ggvartype.Rd man/gnomeR-package.Rd man/gnomer_colors.Rd man/gnomer_cols.Rd man/gnomer_pal.Rd man/gnomer_palette.Rd man/gnomer_palettes.Rd man/impact_gene_info.Rd man/mut.Rd man/mutation_viz.Rd man/oncokb.Rd man/panel_names.Rd man/pathways.Rd man/pipe.Rd man/plot_oncoprint.Rd man/recode_alias.Rd man/reformat_cna.Rd man/resolve_alias.Rd man/scale_color_pancan.Rd man/scale_fill_pancan.Rd man/seg.Rd man/specify_impact_panels.Rd man/substrRight.Rd man/summarize_by_gene.Rd man/tbl_genomic.Rd man/tcga_genes.Rd man/tcga_samples.Rd man/ti_341.Rd man/ti_410.Rd man/ti_468.Rd tests/spelling.R tests/testthat.R tests/testthat/helper_dat.R 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-plots.R tests/testthat/test-recode-alias.R tests/testthat/test-specify-panel.R tests/testthat/test-summarize-by-gene.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
AxelitoMartin/gnomeR documentation built on April 21, 2022, 3:01 p.m.