CaMutQC

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see CaMutQC.

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

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-6072-599X

Maintainer: Xin Wang <sylviawang555 at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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 1.4.5

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

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

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Depends On 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_1.4.5.tar.gz

Windows Binary (x86_64) CaMutQC_1.4.5.zip (64-bit only)

macOS Binary (x86_64) CaMutQC_1.4.5.tgz

macOS Binary (arm64) CaMutQC_1.4.5.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

Old Source Packages for BioC 3.21 Source Archive