All Projects → PoisonAlien → Maftools

PoisonAlien / Maftools

Licence: mit
Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

Programming Languages

r
7636 projects

Projects that are alternatives of or similar to Maftools

revolver
REVOLVER - Repeated Evolution in Cancer
Stars: ✭ 52 (-79.12%)
Mutual labels:  cancer-genomics
Music2
identifying mutational significance in cancer genomes
Stars: ✭ 49 (-80.32%)
Mutual labels:  cancer-genomics
Lollipops
Lollipop-style mutation diagrams for annotating genetic variations.
Stars: ✭ 147 (-40.96%)
Mutual labels:  cancer-genomics
civic-client
Web client for CIViC: Clinical Interpretations of Variants in Cancer
Stars: ✭ 49 (-80.32%)
Mutual labels:  cancer-genomics
Sv Callers
Snakemake-based workflow for detecting structural variants in WGS data
Stars: ✭ 28 (-88.76%)
Mutual labels:  cancer-genomics
Somaticseq
An ensemble approach to accurately detect somatic mutations using SomaticSeq
Stars: ✭ 119 (-52.21%)
Mutual labels:  cancer-genomics
SigProfilerPlotting
SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
Stars: ✭ 31 (-87.55%)
Mutual labels:  cancer-genomics
Awesome Cancer Variant Databases
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Stars: ✭ 212 (-14.86%)
Mutual labels:  cancer-genomics
Agfusion
Python package to annotate and visualize gene fusions.
Stars: ✭ 36 (-85.54%)
Mutual labels:  cancer-genomics
Lancet
Microassembly based somatic variant caller for NGS data
Stars: ✭ 134 (-46.18%)
Mutual labels:  cancer-genomics
Pygeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Stars: ✭ 261 (+4.82%)
Mutual labels:  cancer-genomics
Getting Started With Genomics Tools And Resources
Unix, R and python tools for genomics and data science
Stars: ✭ 587 (+135.74%)
Mutual labels:  cancer-genomics
Tybalt
Training and evaluating a variational autoencoder for pan-cancer gene expression data
Stars: ✭ 126 (-49.4%)
Mutual labels:  cancer-genomics
SigProfilerExtractor
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…
Stars: ✭ 86 (-65.46%)
Mutual labels:  cancer-genomics
Pcgr
Personal Cancer Genome Reporter (PCGR)
Stars: ✭ 168 (-32.53%)
Mutual labels:  cancer-genomics
pathway-mapper
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Stars: ✭ 47 (-81.12%)
Mutual labels:  cancer-genomics
Msisensor
microsatellite instability detection using tumor only or paired tumor-normal data
Stars: ✭ 103 (-58.63%)
Mutual labels:  cancer-genomics
Delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Stars: ✭ 247 (-0.8%)
Mutual labels:  cancer-genomics
Ideogram
Chromosome visualization for the web
Stars: ✭ 181 (-27.31%)
Mutual labels:  cancer-genomics
Somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Stars: ✭ 128 (-48.59%)
Mutual labels:  cancer-genomics

maftools - An R package to summarize, analyze and visualize MAF files

bioc bioc bioc GitHub closed issues Lifecycle: stable Lines Of Code

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)

Powered By

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].