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Bioconductor - maftools (development version)

maftools

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

Summarize, Analyze and Visualize MAF Files

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
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")
Details biocViews Classification, DNASeq, DataRepresentation, DriverMutation, FeatureExtraction, FunctionalGenomics, Sequencing, Software, SomaticMutation, Survival, VariantAnnotation, Visualization Version 2.25.10 In Bioconductor since BioC 3.4 (R-3.3) (8.5 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 See More 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 CaMutQC, CIMICE, katdetectr, musicatk, aplotExtra, pathwayTMB, PMAPscore, ProgModule, Rediscover, sigminer, SMDIC, ssMutPA Suggests Me GenomicDataCommons, MultiAssayExperiment, survtype, TCGAbiolinks, oncoPredict Links To Me Build Report Build Report Package Archives

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

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