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

Need some help? Ask on the Bioconductor Support site!

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

Suggests	knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report

Package Archives

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

Source Package	CaMutQC_1.0.0.tar.gz
Windows Binary (x86_64)	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