Files in umccr/gpgr
Genomics Platform Group Reporting
.Rbuildignore
.Rinstignore
.bumpversion.cfg
.dockerignore
.dvc/.gitignore
.dvc/config
.dvcignore
.github/.gitignore
.github/workflows/deploy.yaml
.gitignore
.pre-commit-config.yaml
DESCRIPTION
Dockerfile
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/globals.R
R/oncokb.R
R/oncoviral.R
R/purple.R
R/rmd.R
R/sv.R
R/umccrise.R
R/utils.R
R/utils_shortcuts.R
R/vignettes.R
README.Rmd
README.md
conda/env/lock/conda-lock.yml
conda/env/lock/gpgr-linux-64.lock
conda/env/yaml/condabuild.yaml
conda/env/yaml/gpgr.yaml
conda/env/yaml/pkgdown.yaml
conda/recipe/build.sh
conda/recipe/meta.yaml
data-raw/EFFECT_ABBREVIATIONS.R
data-raw/umccr_cancer_genes.R
data/EFFECT_ABBREVIATIONS.rda
gpgr.Rproj
inst/cli/canrep.R
inst/cli/gpgr.R
inst/extdata/.gitignore
inst/extdata/purple/.gitignore
inst/extdata/purple/purple.cnv.gene.tsv.dvc
inst/extdata/purple/purple.cnv.germline.tsv.dvc
inst/extdata/purple/purple.cnv.somatic.tsv.dvc
inst/extdata/purple/purple.purity.tsv.dvc
inst/extdata/purple/purple.qc.dvc
inst/extdata/purple/purple.somatic.vcf.gz.dvc
inst/extdata/purple/purple.version.dvc
inst/extdata/ref/.gitignore
inst/extdata/ref/somatic_panel-v24.03.0.tsv.dvc
inst/extdata/ref/umccr_cancer_genes_hg38_coding.bed.gz
inst/extdata/sash/.gitignore
inst/extdata/sash/sv.prioritised.tsv.dvc
inst/extdata/umccrise/snv/.gitignore
inst/extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz.dvc
inst/extdata/umccrise/sv/.gitignore
inst/extdata/umccrise/sv/manta.tsv.dvc
inst/extdata/umccrise/sv/manta.vcf.gz.dvc
inst/extdata/virusbreakend/.gitignore
inst/extdata/virusbreakend/virusbreakend.vcf.dvc
inst/extdata/virusbreakend/virusbreakend.vcf.summary.tsv.dvc
inst/rmd/umccrise/.gitignore
inst/rmd/umccrise/_navbar.html
inst/rmd/umccrise/cancer_report.Rmd
inst/rmd/umccrise/render.R
inst/rmd/umccrise/render.sh
inst/rmd/umccrise/style.css
inst/rmd/umccrise/vccc_small.jpg
man/EFFECT_ABBREVIATIONS.Rd
man/abbreviate_effect.Rd
man/af_summary.Rd
man/bcftools_stats_plot.Rd
man/cancer_rmd.Rd
man/count_pieces.Rd
man/date_log.Rd
man/dragen_hrd.Rd
man/get_oncokb_genes.Rd
man/gpgr-package.Rd
man/hrd_results_tabs.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_cnv_tsv.Rd
man/process_sv.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/read_oncokb.Rd
man/session_info_kable.Rd
man/split_double_col.Rd
man/tidyeval.Rd
man/tsv_is_empty.Rd
man/vcf_is_empty.Rd
man/virusbreakend_summary_read.Rd
man/virusbreakend_vcf_read.Rd
man/write_jsongz.Rd
man/write_tsvgz.Rd
man/write_tsvjsongz.Rd
pkgdown/_pkgdown.yml
tests/testthat.R
tests/testthat/test-roxytest-testexamples-oncoviral.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/devnotes.Rmd
vignettes/purple.Rmd
vignettes/style.css
