CaMutQC
This is the released version of CaMutQC; for the devel version, see CaMutQC.
An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
Bioconductor version: Release (3.23)
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.
Maintainer: Xin Wang <sylviawang555 at gmail.com>
citation("CaMutQC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneTarget, QualityControl, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| 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, shiny |
| 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_1.8.0.tar.gz |
| Windows Binary (x86_64) | CaMutQC_1.8.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CaMutQC_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | CaMutQC_1.8.0.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 |