maftools

DOI: 10.18129/B9.bioc.maftools    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see maftools.

Summarize, Analyze and Visualize MAF Files

Bioconductor version: 3.15

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]

Maintainer: Anand Mayakonda <anand_mt at hotmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	Classification, DNASeq, DataRepresentation, DriverMutation, FeatureExtraction, FunctionalGenomics, Sequencing, Software, SomaticMutation, Survival, VariantAnnotation, Visualization
Version	2.12.0
In Bioconductor since	BioC 3.4 (R-3.3) (6 years)
License	MIT + file LICENSE
Depends	R (>= 3.3)
Imports	data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy
LinkingTo	Rhtslib, zlibbioc
Suggests	berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, pheatmap, curl
SystemRequirements	GNU make
Enhances
URL	https://github.com/PoisonAlien/maftools
BugReports	https://github.com/PoisonAlien/maftools/issues
Depends On Me
Imports Me	CIMICE, musicatk, TCGAbiolinksGUI, TCGAWorkflow
Suggests Me	GenomicDataCommons, MultiAssayExperiment, survtype, TCGAbiolinks
Links To Me
Build Report

Package Archives

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

Source Package	maftools_2.12.0.tar.gz
Windows Binary	maftools_2.12.0.zip
macOS Binary (x86_64)	maftools_2.12.0.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