Files in likelet/CaMutQC

An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/TMB.R R/getVarClass.R R/getVarFeature.R R/jointMAF.R R/mutFilterAdj.R R/mutFilterCan.R R/mutFilterCom.R R/mutFilterDB.R R/mutFilterNormalDP.R R/mutFilterPON.R R/mutFilterQual.R R/mutFilterRef.R R/mutFilterReg.R R/mutFilterSB.R R/mutFilterTech.R R/mutFilterType.R R/mutSelection.R R/processMut.R R/readBed.R R/readINFO.R R/selectMut.R R/selectTrans.R R/toMesKit.R R/tomaftools.R R/vcfToMAF.R README.md

inst/CITATION

inst/NEWS.md

inst/extdata/Multi-caller/WES_EA_T_1.MuSE.vep.vcf

inst/extdata/Multi-caller/WES_EA_T_1_varscan_filter_snp.vep.vcf

inst/extdata/PON_test.txt

inst/extdata/Panel_gene/FoundationOne_genelist.txt

inst/extdata/Panel_gene/MSK-IMPACT_gene_v1_341.txt

inst/extdata/Panel_gene/MSK-IMPACT_gene_v2_410.txt

inst/extdata/Panel_gene/MSK-IMPACT_gene_v3_468.txt

inst/extdata/Panel_gene/Pan-cancer_genelist.txt

inst/extdata/TSGenelist.txt

inst/extdata/WES_EA_T_1_mutect2.vep.vcf

inst/extdata/bed/panel_hg19/FlCDx-hg19.rds

inst/extdata/bed/panel_hg19/MSK_v1-hg19.rds

inst/extdata/bed/panel_hg19/MSK_v2-hg19.rds

inst/extdata/bed/panel_hg19/MSK_v3-hg19.rds

inst/extdata/bed/panel_hg19/Pan-cancer-hg19.rds

inst/extdata/bed/panel_hg38/FlCDx-hg38.rds

inst/extdata/bed/panel_hg38/MSK_v1-hg38.rds

inst/extdata/bed/panel_hg38/MSK_v2-hg38.rds

inst/extdata/bed/panel_hg38/MSK_v3-hg38.rds

inst/extdata/bed/panel_hg38/Pan-cancer-hg38.rds

inst/extdata/clin.txt

inst/extdata/noncoding.txt

inst/rmd/CaMutQC-FilterReport.Rmd

inst/script/DATASETS

man/calTMB.Rd man/mutFilterAdj.Rd man/mutFilterCan.Rd man/mutFilterCom.Rd man/mutFilterDB.Rd man/mutFilterNormalDP.Rd man/mutFilterPON.Rd man/mutFilterQual.Rd man/mutFilterRef.Rd man/mutFilterReg.Rd man/mutFilterSB.Rd man/mutFilterTech.Rd man/mutFilterType.Rd man/mutSelection.Rd man/processMut.Rd man/toMesKit.Rd man/tomaftools.Rd man/vcfToMAF.Rd vignettes/CaMutQC-manual.Rmd

vignettes/CaMutQC-workflow.png

vignettes/CaMutQC_logo.png

vignettes/Union_strategy.png

likelet/CaMutQC documentation built on April 3, 2024, 9:06 a.m.