Data

Tools

Indexes

Applications

Experiments

Open Source Science

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

https://github.com/poisonalien/maftools

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    3 of 31 committers (9.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.9%) to scientific vocabulary

Keywords

bioinformatics cancer-genome-atlas cancer-genomics genomics maf-files r tcga

Keywords from Contributors

bioconductor-package gene bioconductor core-package u24ca289073 core-services derfinder rnaseq mass-spectrometry metabolomics
Last synced: 6 months ago · JSON representation

Repository

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

Basic Info
Statistics
  • Stars: 472
  • Watchers: 21
  • Forks: 223
  • Open Issues: 8
  • Releases: 1
Topics
bioinformatics cancer-genome-atlas cancer-genomics genomics maf-files r tcga
Created about 10 years ago · Last pushed 8 months ago
Metadata Files
Readme License

README.md

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

GitHub closed issues R-CMD-check

Introduction

maftools is a comprehensive toolkit for processing somatic variants from cohort-based cancer genomic studies. maftools offers over 80 functions to perform the most commonly required tasks in cancer genomics, using MAF as the only input file type.

Installation

```{r}

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.

Primary applications

maftools is extremely easy to use, starting with importing an MAF file along with the associated clinical data. Once the data is successfully imported, the resulting MAF object can be passed to various functions. Key applications include:

Besides the MAF files, maftools can handle sequencing alignment BAM files, copy number output from GISTIC and mosdepth. Please refer to the package documentation sections below to learn more.

Moreover, analyzing all 33 TCGA cohorts along with the harmonized clinical data is a breeze.

  • A single command tcgaLoad will import the desired TCGA cohort thereby avoiding costly time spent on data mining from public databases.
  • Please refer to an associated software package TCGAmutations that provides ready to use MAF objects for 33 TCGA cohorts and 2427 cell line profiles from CCLE - along with relevant clinical information for all sequenced samples.

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 Fomats | Data portals | Annotation tools | |--------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------| | Mutation Annotation Format | TCGA | vcf2maf - for converting your VCF files to MAF | | Variant Call Format | ICGC | annovar2maf - for converting annovar output files to MAF | | ICGC Simple Somatic Mutation Format | Broad Firehose | bcftools csq - Rapid annotations of VCF files with variant consequences | | | cBioPortal | Annovar | | | PeCan | Funcotator | | | CIViC - Clinical interpretation of variants in cancer | | | | DGIdb - Information on drug-gene interactions and the druggable genome | |

Useful packages/tools

Below are some more useful software packages for somatic variant analysis

  • 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

Owner

  • Name: Anand Mayakonda
  • Login: PoisonAlien
  • Kind: user
  • Location: Heidelberg

Cancer genomics and Bioinformatics.

GitHub Events

Total
  • Issues event: 69
  • Watch event: 23
  • Issue comment event: 131
  • Push event: 11
  • Pull request event: 4
  • Fork event: 8
Last Year
  • Issues event: 69
  • Watch event: 23
  • Issue comment event: 131
  • Push event: 11
  • Pull request event: 4
  • Fork event: 8

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 751
  • Total Committers: 31
  • Avg Commits per committer: 24.226
  • Development Distribution Score (DDS): 0.156
Past Year
  • Commits: 13
  • Committers: 2
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.154
Top Committers
Name Email Commits
PoisonAlien a****3@g****m 634
ShixiangWang w****x@s****n 20
Anand Mayakonda a****t@h****m 17
Nitesh Turaga n****a@g****m 14
bio_sun b****n@f****m 12
rdmorin r****n@s****a 10
Herve Pages h****s@f****g 4
zmi z****k@g****m 4
J Wokaty j****y@s****u 4
Anand Mayakonda a****a@b****l 3
Yoshihiro Ishida y****a@k****p 3
vobencha v****n@r****g 2
Eliseo Martelli me@e****t 2
Hervé Pagès h****s@f****g 2
Zuguang Gu j****o@g****m 2
omarelashkar o****r@h****m 2
vobencha v****a@g****m 2
zhangyz1997 z****7 1
moxgreen i****s@g****m 1
mattdowle m****e@g****m 1
lshep l****d@r****g 1
Anand Mayakonda a****a@d****e 1
Martin Morgan m****n@f****g 1
anand_mt a****d@w****l 1
kaigu1990 g****2@1****m 1
igor 6****t 1
bing s****6@1****m 1
Z_Wael z****s@g****m 1
Qinsi l****i@g****m 1
LiNk-NY m****z@r****g 1
and 1 more...
Committer Domains (Top 20 + Academic)
roswellpark.org: 3 fhcrc.org: 2 126.com: 1 163.com: 1 dkfz-heidelberg.de: 1 fredhutch.org: 1 eliseomartelli.it: 1 kuhp.kyoto-u.ac.jp: 1 sph.cuny.edu: 1 sfu.ca: 1 foxmail.com: 1 shanghaitech.edu.cn: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 198
  • Total pull requests: 14
  • Average time to close issues: 3 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 137
  • Total pull request authors: 7
  • Average comments per issue: 4.03
  • Average comments per pull request: 0.5
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 42
  • Pull requests: 4
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 12 hours
  • Issue authors: 31
  • Pull request authors: 2
  • Average comments per issue: 1.29
  • Average comments per pull request: 0.25
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • DarioS (7)
  • rdmorin (6)
  • wangzunq (6)
  • HiraDatascience (6)
  • crazyhottommy (6)
  • shirleydaidai (5)
  • xiw588 (4)
  • zayni (4)
  • lbeltrame (4)
  • MaryGoAround (3)
  • kpjonsson (2)
  • juferban (2)
  • WangYe661 (2)
  • Jwang412 (2)
  • raman91 (2)
Pull Request Authors
  • rdmorin (3)
  • PoisonAlien (2)
  • eolaniru (2)
  • eliseomartelli (2)
  • mattions (2)
  • fabianjkrueger (2)
  • ccchang0111 (1)
Top Labels
Issue Labels
stale (45) enhancement (10) bug (10) add feature (4) wontfix (2) help wanted (1) followup (1)
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • bioconductor 287,059 total
  • Total dependent packages: 9
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 9
  • Total maintainers: 1
bioconductor.org: maftools

Summarize, Analyze and Visualize MAF Files

  • Versions: 5
  • Dependent Packages: 9
  • Dependent Repositories: 0
  • Downloads: 287,059 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 0.0%
Stargazers count: 0.1%
Average: 1.5%
Downloads: 7.2%
Maintainers (1)
anand_mt@hotmail.com
Last synced: 6 months ago
proxy.golang.org: github.com/PoisonAlien/maftools
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/poisonalien/maftools
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
DESCRIPTION cran
  • R >= 3.3 depends
  • DNAcopy * imports
  • RColorBrewer * imports
  • Rhtslib * imports
  • data.table * imports
  • grDevices * imports
  • methods * imports
  • survival * imports
  • BSgenome * suggests
  • BSgenome.Hsapiens.UCSC.hg19 * suggests
  • Biostrings * suggests
  • GenomicRanges * suggests
  • IRanges * suggests
  • MultiAssayExperiment * suggests
  • NMF * suggests
  • R.utils * suggests
  • RaggedExperiment * suggests
  • S4Vectors * suggests
  • berryFunctions * suggests
  • curl * suggests
  • knitr * suggests
  • mclust * suggests
  • pheatmap * suggests
  • rmarkdown * suggests