The maftools from kgaonkar6

maftools's Introduction

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)