Files in mskilab/casereport
casereport: Whole-genome + transcription based report for cancer genomes
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/casereport.R
R/config.R
R/fusion.gallery.R
R/pmkb-utils.R
R/snvs.R
R/sv.gallery.R
R/utils.R
README.md
exec/run.sh
flow.deploy
inst/extdata/AML.signatures.txt
inst/extdata/BE.signatures.txt
inst/extdata/BLCA.signatures.txt
inst/extdata/BRCA.signatures.txt
inst/extdata/CESC.signatures.txt
inst/extdata/COAD.signatures.txt
inst/extdata/ESAD.signatures.txt
inst/extdata/ESSC.signatures.txt
inst/extdata/G32831/G32831.Detroit_562.chr11.window.hets.txt
inst/extdata/G32831/G32831.Detroit_562.chr11.window.rds
inst/extdata/G32831/G32831.Detroit_562.vcf
inst/extdata/G32831/annotated.bcf
inst/extdata/G32831/complex.rds
inst/extdata/G32831/deconstructSigs.out.rds
inst/extdata/G32831/fusions.rds
inst/extdata/G32831/germline-annotated.bcf
inst/extdata/G32831/germline-annotated.bcf.csi
inst/extdata/G32831/jabba.simple.rds
inst/extdata/G32831/variants.out.txt.gz
inst/extdata/GBM.signatures.txt
inst/extdata/HNSC.signatures.txt
inst/extdata/KICH.signatures.txt
inst/extdata/KIRC.signatures.txt
inst/extdata/KIRP.signatures.txt
inst/extdata/LGG.signatures.txt
inst/extdata/LIHC.signatures.txt
inst/extdata/LUAD.signatures.txt
inst/extdata/LUSC.signatures.txt
inst/extdata/MALY.signatures.txt
inst/extdata/MELA.signatures.txt
inst/extdata/OV.signatures.txt
inst/extdata/PACA.signatures.txt
inst/extdata/PRAD.signatures.txt
inst/extdata/SARC.signatures.txt
inst/extdata/STAD.signatures.txt
inst/extdata/SnpEff_module/run.sh
inst/extdata/SnpEff_module/snpEff.jar
inst/extdata/SnpEff_module/wgs.report.rmd
inst/extdata/THCA.signatures.txt
inst/extdata/UCEC.signatures.txt
inst/extdata/all.signatures.txt
inst/extdata/cancerGeneList.tsv
inst/extdata/case_report_module/wgs.report.rmd
inst/extdata/case_report_module/wgs.report.table.rmd
inst/extdata/cgc.tsv
inst/extdata/cohort.metadata.tsv.gz
inst/extdata/ddr_pearl2015.tsv
inst/extdata/gt.ge.hg19.rds
inst/extdata/hg19.broad.chrom.sizes
inst/extdata/hg19.cytoband.txt
inst/extdata/hg38.chrom.sizes
inst/extdata/hg38.cytoband.txt
inst/extdata/hrdetect.og.txt
inst/extdata/mock.gencode.gtf
inst/extdata/onc.rds
inst/extdata/oncokb_biomarker_drug_associations.tsv
inst/extdata/ot_scores_cohort.rds
inst/extdata/pmkb-interpretations-06-11-2021.csv
inst/extdata/pmkb-tier.csv
inst/extdata/pmkb-tier.tsv
inst/extdata/sig.metadata.txt
inst/extdata/surface.rds
inst/extdata/sv.burden.txt
inst/extdata/tsg.rds
inst/extdata/ug.txt
inst/extdata/wgs.report.rmd
man/annotate_pmkb_entries_as_tsg_or_onc.Rd
man/annotate_with_pmkb.Rd
man/annotated_bcf_to_oncotable.Rd
man/check_GRanges_compatibility.Rd
man/check_file.Rd
man/circos.Rd
man/cn.plot.Rd
man/compute_rna_quantiles.Rd
man/counts.to.allele.cn.Rd
man/covcbs.Rd
man/create.summary.Rd
man/create_genes_gtrack.Rd
man/deconstructsigs_histogram.Rd
man/extract_variant_types_from_pmkb.Rd
man/filter.snpeff.Rd
man/fusion.plot.Rd
man/fusion.table.Rd
man/fusion.wrapper.Rd
man/gallery.wrapper.Rd
man/get_gene_ampdel_annotations.Rd
man/get_gene_copy_numbers.Rd
man/get_oncokb_annotations.Rd
man/get_oncokb_gene_entry_url.Rd
man/get_oncokb_response.Rd
man/get_pmkb_dt.Rd
man/get_pmkb_tier_table.Rd
man/grab.agtrack.Rd
man/grab.gene.ranges.Rd
man/grab.hets.Rd
man/grab.window.Rd
man/makeSummaryTable.Rd
man/oncoprint.Rd
man/oncotable.Rd
man/plot_expression_histograms.Rd
man/pp_plot.Rd
man/ppgrid.Rd
man/ridge.plot.Rd
man/rna.waterfall.plot.Rd
man/rna_quantile.Rd
man/rna_reformat.Rd
man/set_param.Rd
man/star2grl.Rd
man/summarize_cases.Rd
man/sv.plot.Rd
man/test_oncokb_api.Rd
man/wgs.circos.Rd
man/wgs.report.Rd
man/wgs_gtrack.Rd
optimize_png.py
tests/testthat.R
tests/testthat/test-casereport.R
tests/testthat/test-sv.gallery.R
wgs.casereport.task
wgs.report
wgs.report.rmd
