CaMutQC

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


Bioconductor version: Release (3.19)

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.

Author: Xin Wang [aut, cre]

Maintainer: Xin Wang <sylviawang555 at gmail.com>

Citation (from within R, enter citation("CaMutQC")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CaMutQC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CaMutQC")
Manual HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneTarget, QualityControl, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-3
Depends R (>= 4.0.0)
Imports ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr, DT, MesKit, maftools, data.table, utils, stats, methods, tidyr
System Requirements
URL https://github.com/likelet/CaMutQC
Bug Reports https://github.com/likelet/CaMutQC/issues
See More
Suggests knitr, rmarkdown, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CaMutQC_1.0.0.tar.gz
Windows Binary CaMutQC_1.0.0.zip
macOS Binary (x86_64) CaMutQC_1.0.0.tgz
macOS Binary (arm64) CaMutQC_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CaMutQC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CaMutQC
Bioc Package Browser https://code.bioconductor.org/browse/CaMutQC/
Package Short Url https://bioconductor.org/packages/CaMutQC/
Package Downloads Report Download Stats