Package: CaMutQC 1.8.0

Xin Wang

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

CaMutQC is able to filter false positive mutations generated due to technical issues, as well as to select candidate cancer mutations through a series of well-structured functions by labeling mutations with various flags. And a detailed and vivid filter report will be offered after completing a whole filtration or selection section. Also, CaMutQC integrates serveral methods and gene panels for Tumor Mutational Burden (TMB) estimation.

Authors:Xin Wang [aut, cre]

CaMutQC_1.8.0.tar.gz
CaMutQC_1.8.0.zip(r-4.7)CaMutQC_1.8.0.zip(r-4.6)CaMutQC_1.8.0.zip(r-4.5)
CaMutQC_1.8.0.tgz(r-4.6-any)CaMutQC_1.8.0.tgz(r-4.5-any)
CaMutQC_1.8.0.tar.gz(r-4.7-any)CaMutQC_1.8.0.tar.gz(r-4.6-any)
CaMutQC_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CaMutQC/json (API)

# Install 'CaMutQC' in R:

install.packages('CaMutQC', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/likelet/camutqc/issues

On BioConductor:CaMutQC-1.9.0(bioc 3.24)CaMutQC-1.8.0(bioc 3.23)

software qualitycontrol genetarget cancer-genomics somatic-mutations

5.86 score 8 stars 3 scripts 224 downloads 18 exports 158 dependencies

Last updated from:fa2c753916 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	248
linux-devel-x86_64	NOTE	365
source / vignettes	OK	369
linux-release-x86_64	NOTE	365
macos-release-arm64	NOTE	245
macos-oldrel-arm64	NOTE	284
windows-devel	NOTE	263
windows-release	NOTE	324
windows-oldrel	NOTE	240
wasm-release	OK	201

Exports:calTMB mutFilterAdj mutFilterCan mutFilterCom mutFilterDB mutFilterNormalDP mutFilterPON mutFilterQual mutFilterRef mutFilterReg mutFilterSB mutFilterTech mutFilterType mutSelection processMut tomaftools toMesKit vcfToMAF

Dependencies:aisdk AnnotationDbi ape aplot askpass base64enc Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem callr circlize cli clue cluster clusterProfiler codetools colorspace ComplexHeatmap cowplot cpp11 crayon crosstalk curl data.table DBI digest DNAcopy doParallel DOSE dplyr DT enrichit enrichplot evaluate farver fastmap fastmatch fontawesome fontBitstreamVera fontLiberation fontquiver foreach fs gdtools generics GetoptLong ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggridges ggtangle ggtree GlobalOptions glue GO.db GOSemSim gridGraphics gson gtable highr htmltools htmlwidgets httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling later lattice lazyeval lifecycle maftools magrittr MASS Matrix matrixStats mclust memoise memuse MesKit mgcv mime nlme openssl org.Hs.eg.db otel patchwork permute phangorn pheatmap pillar pinfsc50 pkgconfig plyr png polyclip pracma processx promises ps purrr quadprog qvalue R6 rappdirs RColorBrewer Rcpp reshape2 Rhtslib rjson rlang rmarkdown RSQLite S4Vectors S7 sass scales scatterpie Seqinfo shape stringi stringr survival sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr utf8 vcfR vctrs vegan viridisLite withr xfun XVector yaml yulab.utils

CaMutQC: Cancer Somatic Mutation Quality Control

Xin Wang [email protected]

Rendered fromCaMutQC-manual.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2025-10-20
Started: 2021-11-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
calTMB	calTMB
mutFilterAdj	mutFilterAdj
mutFilterCan	mutFilterCan
mutFilterCom	mutFilterCom
mutFilterDB	mutFilterDB
mutFilterNormalDP	mutFilterNormalDP
mutFilterPON	mutFilterPON
mutFilterQual	mutFilterQual
mutFilterRef	mutFilterRef
mutFilterReg	mutFilterReg
mutFilterSB	mutFilterSB
mutFilterTech	mutFilterTech
mutFilterType	mutFilterType
mutSelection	mutSelection
processMut	processMut
tomaftools	tomaftools
toMeskit	toMesKit
vcfToMAF	vcfToMAF