maftools

DOI: 10.18129/B9.bioc.maftools    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see maftools.

Summarize, Analyze and Visualize MAF Files

Bioconductor version: 3.9

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: person("Anand","Mayakonda", role = c("aut","cre"), email = "[email protected]"), comment = c(ORCID = '0000-0003-1162-687X')

Maintainer: Anand Mayakonda <anand_mt at hotmail.com>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, DNASeq, DataRepresentation, DriverMutation, FeatureExtraction, FunctionalGenomics, Sequencing, Software, SomaticMutation, Survival, VariantAnnotation, Visualization
Version	2.0.16
In Bioconductor since	BioC 3.4 (R-3.3) (3 years)
License	MIT + file LICENSE
Depends	R (>= 3.3)
Imports	data.table, cometExactTest, RColorBrewer, NMF, methods, wordcloud, grDevices, survival
LinkingTo
Suggests	knitr, rmarkdown, BSgenome, Biostrings, mclust, rjson
SystemRequirements
Enhances
URL	https://github.com/PoisonAlien/maftools
BugReports	https://github.com/PoisonAlien/maftools/issues
Depends On Me
Imports Me	TCGAbiolinksGUI, TCGAWorkflow
Suggests Me	survtype, TCGAbiolinks
Links To Me
Build Report

Package Archives

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

Source Package	maftools_2.0.16.tar.gz
Windows Binary	maftools_2.0.16.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	maftools_2.0.16.tgz
Source Repository	git clone https://git.bioconductor.org/packages/maftools
Source Repository (Developer Access)	git clone [email protected]:packages/maftools
Package Short Url	https://bioconductor.org/packages/maftools/
Package Downloads Report	Download Stats