maftools
Summarize, Analyze and Visualize MAF Files
Bioconductor version: Release (3.20)
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("maftools")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, DNASeq, DataRepresentation, DriverMutation, FeatureExtraction, FunctionalGenomics, Sequencing, Software, SomaticMutation, Survival, VariantAnnotation, Visualization |
| Version | 2.22.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.3) |
| Imports | data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy, pheatmap |
| System Requirements | GNU make |
| 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, curl |
| Linking To | Rhtslib, zlibbioc |
| Enhances | |
| Depends On Me | GNOSIS |
| Imports Me | CaMutQC, CIMICE, katdetectr, musicatk, TCGAWorkflow, 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.
| Source Package | maftools_2.22.0.tar.gz |
| Windows Binary (x86_64) | maftools_2.22.0.zip |
| macOS Binary (x86_64) | maftools_2.22.0.tgz |
| macOS Binary (arm64) | maftools_2.22.0.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 |