CaMutQC
This is the development version of CaMutQC; for the stable release version, see CaMutQC.
An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
Bioconductor version: Development (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:
Maintainer: Xin Wang <sylviawang555 at gmail.com>
citation("CaMutQC")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneTarget, QualityControl, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 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 |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CaMutQC_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |