maftools

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see maftools.

Summarize, Analyze and Visualize MAF Files


Bioconductor version: 3.7

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 <anand_mt at hotmail.com>

Maintainer: Anand Mayakonda <anand_mt at hotmail.com>

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

Installation

To install this package, start R (version "3.5") 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")
Summarize, Analyze and Visualize MAF Files HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Classification, DNASeq, DataRepresentation, DriverMutation, FeatureExtraction, FunctionalGenomics, Sequencing, Software, SomaticMutation, Survival, VariantAnnotation, Visualization
Version 1.6.15
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License MIT + file LICENSE
Depends R (>= 3.3)
Imports data.table, ggplot2 (>= 2.0), cowplot, cometExactTest, RColorBrewer, NMF, ggrepel, methods, ComplexHeatmap, mclust, VariantAnnotation, Biostrings, Rsamtools, rjson, grid, wordcloud, grDevices, changepoint, gridExtra, survival
System Requirements
URL https://github.com/PoisonAlien/maftools
Bug Reports https://github.com/PoisonAlien/maftools/issues
See More
Suggests knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me TCGAbiolinksGUI, TCGAWorkflow
Suggests Me TCGAbiolinks
Links To Me
Build Report Build Report

Package Archives

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

Source Package maftools_1.6.15.tar.gz
Windows Binary maftools_1.6.15.zip
Mac OS X 10.11 (El Capitan) maftools_1.6.15.tgz
Source Repository git clone https://git.bioconductor.org/packages/maftools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/maftools
Bioc Package Browser https://code.bioconductor.org/browse/maftools/
Package Short Url https://bioconductor.org/packages/maftools/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive