maftools
Summarize, Analyze and Visualize MAF Files
Bioconductor version: 3.23 · Package version: 2.28.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("maftools")Details
| Maintainer | Anand Mayakonda <anand_mt@hotmail.com> |
| Author | Anand Mayakonda [aut, cre] (ORCID: <https://orcid.org/0000-0003-1162-687X>) |
| License | MIT + file LICENSE |
| URL | https://github.com/PoisonAlien/maftools |
| Bug Reports | https://github.com/PoisonAlien/maftools/issues |
| System Requirements | GNU make, curl |
| Downloads rank | 3155 |
| Source branch | RELEASE_3_23 |
| biocViews | Classification, DNASeq, DataRepresentation, DriverMutation, FeatureExtraction, FunctionalGenomics, Sequencing, Software, SomaticMutation, Survival, VariantAnnotation, Visualization |
Documentation
- maftools : Summarize, Analyze and Visualize MAF Files
- Customizing oncoplots
- Personlaized cancer report
- Copy number analysis
Download
Dependencies
Depends: R (>= 4.1.0)
Imports: data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy, pheatmap
LinkingTo: Rhtslib
Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors
Reverse dependencies
Depends On Me (1): GNOSIS
Imports Me (9): aplotExtra, CaMutQC, CIMICE, katdetectr, musicatk, Rediscover, sigminer, SMDIC, ssMutPA
Suggests Me (5): GenomicDataCommons, IOBR, MultiAssayExperiment, survtype, TCGAbiolinks