PoisonAlien / Maftools
Licence: mit
Summarize, Analyze and Visualize MAF files from TCGA or in house studies.
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r
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maftools - An R package to summarize, analyze and visualize MAF files
Introduction
maftools
provides a comprehensive set of functions for processing MAF files and to perform most commonly used analyses in cancer genomics. See here for a detailed usage and a case study.
Installation
#Install from Bioconductor repository
BiocManager::install("maftools")
#Install from GitHub repository
BiocManager::install("PoisonAlien/maftools")
Getting started: Vignette and a case study
A complete documentation of maftools using TCGA LAML as a case study can be found here.
Citation
Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. 2018. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Research. PMID: 30341162
Useful links
File formats | Data Portals | Annotation tools |
---|---|---|
Mutation Annotation Format | TCGA | vcf2maf - for converting your VCF files to MAF |
Variant Call Format | ICGC | Ensembl Variant Effect Predictor VEP |
ICGC Simple Somatic Mutation Format | Broad Firehose | Annovar |
cBioPortal | Funcotator | |
CIViC - Clinical interpretation of variants in cancer | ||
DGIdb - Information on drug-gene interactions and the druggable genome |
Similar packages/tools
Below are some more useful software packages for somatic variant analysis (not necessarily similar to maftools)
- TRONCO - Repository of the TRanslational ONCOlogy library (R)
- dndscv - dN/dS methods to quantify selection in cancer and somatic evolution (R)
- cloneevol - Inferring and visualizing clonal evolution in multi-sample cancer sequencing (R)
-
sigminer - Primarily for signature analysis and visualization in R. Supports
maftools
output (R) - GenVisR - Primarily for visualization (R)
- comut - Primarily for visualization (Python)
-
TCGAmutations - pre-compiled curated somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project) that can be loaded into
maftools
(R) - somaticfreq - rapid genotyping of known somatic hotspot variants from the tumor BAM files. Generates a browsable/sharable HTML report. (C)
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