maftools

This is the development version of maftools; for the stable release version, see maftools.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

Summarize, Analyze and Visualize MAF Files

Bioconductor version: Development (3.24)

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

Author: Anand Mayakonda [aut, cre] ORCID: 0000-0003-1162-687X

Maintainer: Anand Mayakonda <anand_mt at hotmail.com>

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

Anand Mayakonda. maftools: Summarize, Analyze and Visualize MAF Files. doi:10.18129/B9.bioc.maftools, R package version 2.29.0, https://bioconductor.org/packages/maftools.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("maftools")

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("maftools")

03: Cancer report	HTML	R Script
04: Copy number analysis	HTML	R Script
01: Summarize, Analyze, and Visualize MAF Files	HTML	R Script
02: Customizing oncoplots	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, DNASeq, DataRepresentation, DriverMutation, FeatureExtraction, FunctionalGenomics, Sequencing, Software, SomaticMutation, Survival, VariantAnnotation, Visualization
Version	2.29.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 years)
License	MIT + file LICENSE
Depends	R (>= 4.1.0)
Imports	data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy, pheatmap
System Requirements	GNU make, curl
URL	https://github.com/PoisonAlien/maftools
Bug Reports	https://github.com/PoisonAlien/maftools/issues

Suggests	berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors
Linking To	Rhtslib
Enhances
Depends On Me	GNOSIS
Imports Me	aplotExtra, CaMutQC, CIMICE, katdetectr, musicatk, Rediscover, sigminer, SMDIC, ssMutPA
Suggests Me	GenomicDataCommons, IOBR, MultiAssayExperiment, survtype, TCGAbiolinks
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	maftools_2.29.0.tar.gz
Windows Binary (x86_64)	maftools_2.29.0.zip
macOS Binary (big-sur-x86_64)	maftools_2.29.0.tgz
macOS Binary (sonoma-arm64)	maftools_2.29.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/maftools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/maftools
Package Short Url	https://bioconductor.org/packages/maftools/
Package Downloads Report	Download Stats