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
