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maftools

Summarize, Analyze and Visualize MAF Files

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") 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")
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 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 2.16.0
In Bioconductor since BioC 3.4 (R-3.3) (7 years)
License MIT + file LICENSE
Depends R (>= 3.3)
Imports data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy
Linking To Rhtslib, zlibbioc
Suggests berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, pheatmap, curl
System Requirements GNU make
Enhances
URL https://github.com/PoisonAlien/maftools
Bug Reports https://github.com/PoisonAlien/maftools/issues
See More
Depends On Me
Imports Me CIMICE, katdetectr, musicatk, 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_2.16.0.tar.gz
Windows Binary maftools_2.16.0.zip
macOS Binary (x86_64) maftools_2.16.0.tgz
macOS Binary (arm64) maftools_2.16.0.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