Files in umccr/gpgr
Genomics Platform Group Reporting

.Rbuildignore
.Rinstignore
.bumpversion.cfg
.github/.gitignore
.github/workflows/pkgdown.yaml
.gitignore
.pre-commit-config.yaml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md R/chord.R R/globals.R R/hrdetect.R R/mutationalpatterns.R R/purple.R R/sv.R R/umccrise.R R/utils.R R/utils_shortcuts.R README.md
_pkgdown.yml
data-raw/EFFECT_ABBREVIATIONS.R data-raw/cosmic_signatures_2015.R data-raw/umccr_cancer_genes.R
data/EFFECT_ABBREVIATIONS.rda
data/cosmic_signatures_2015.rda
deploy/conda-recipe/build.sh
deploy/conda-recipe/meta.yaml
deploy/pkgdown_conda_env.yaml
gpgr.Rproj
inst/extdata/purple/purple.cnv.gene.tsv
inst/extdata/purple/purple.cnv.germline.tsv
inst/extdata/purple/purple.cnv.somatic.tsv
inst/extdata/purple/purple.purity.tsv
inst/extdata/purple/purple.qc
inst/extdata/purple/purple.somatic.vcf.gz
inst/extdata/purple/purple.version
inst/extdata/ref/umccr_cancer_genes_2019-03-20.tsv
inst/extdata/ref/umccr_cancer_genes_hg38_coding.bed.gz
inst/extdata/sigs/v2_2015/Sig/1.png
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inst/extdata/sigs/v3.2_2021-march/SBS/description.tsv
inst/extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz
inst/extdata/umccrise/sv/manta.tsv
inst/extdata/umccrise/sv/manta.vcf.gz
inst/rmd/wgs/.gitignore
inst/rmd/wgs/hrd_detection/run_chord_hrdetect.R
inst/rmd/wgs/umccrise/.gitignore
inst/rmd/wgs/umccrise/_navbar.html
inst/rmd/wgs/umccrise/cancer_report.Rmd
inst/rmd/wgs/umccrise/style.css
inst/rmd/wgs/umccrise/vccc_small.jpg
inst/src/gpgr.R
inst/src/run_chord.sh
inst/src/run_hrdetect.sh
inst/src/run_mutpat.sh
man/EFFECT_ABBREVIATIONS.Rd man/abbreviate_effect.Rd man/af_summary.Rd man/chord_mantavcf2df.Rd man/chord_run.Rd man/cosmic_signatures_2015.Rd man/count_pieces.Rd man/get_genome_obj.Rd man/hrd_results_tabs.Rd man/hrdetect_prep_cnv.Rd man/hrdetect_prep_snvindel.Rd man/hrdetect_prep_sv.Rd man/hrdetect_read_purple_cnv.Rd man/hrdetect_read_snvindel_vcf.Rd man/hrdetect_read_sv_vcf.Rd man/hrdetect_run.Rd man/is_vcf.Rd man/mkdir.Rd man/pkg_exists.Rd man/plot_bnd_sr_pr_tot_hist.Rd man/plot_bnd_sr_pr_tot_lines.Rd man/process_sv.Rd man/purple_cnv_germ_process.Rd man/purple_cnv_germ_read.Rd man/purple_cnv_som_gene_process.Rd man/purple_cnv_som_gene_read.Rd man/purple_cnv_som_process.Rd man/purple_cnv_som_read.Rd man/purple_kataegis.Rd man/purple_purity_read.Rd man/purple_qc_read.Rd man/purple_snv_vcf_read.Rd man/purple_version_read.Rd man/sig_contribution.Rd man/sig_contribution_table.Rd man/sig_count_dbs.Rd man/sig_count_indel.Rd man/sig_count_snv.Rd man/sig_plot_dbs.Rd man/sig_plot_indel.Rd man/sig_plot_snv.Rd man/sig_workflow_run.Rd man/split_double_col.Rd man/tidyeval.Rd man/tsv_is_empty.Rd man/umccrise_read_sv_tsv.Rd man/vcf_is_empty.Rd man/write_jsongz.Rd man/write_tsvgz.Rd man/write_tsvjsongz.Rd tests/testthat.R tests/testthat/test-roxytest-testexamples-chord.R tests/testthat/test-roxytest-testexamples-hrdetect.R tests/testthat/test-roxytest-testexamples-purple.R tests/testthat/test-roxytest-testexamples-sv.R tests/testthat/test-roxytest-testexamples-utils.R
vignettes/.gitignore
vignettes/chord.Rmd vignettes/hrdetect.Rmd vignettes/mutationalpatterns.Rmd vignettes/purple.Rmd
umccr/gpgr documentation built on Nov. 25, 2021, 1:15 p.m.