{"id":15703873,"url":"https://github.com/poisonalien/maftools","last_synced_at":"2025-05-14T04:08:43.533Z","repository":{"id":40693788,"uuid":"49122332","full_name":"PoisonAlien/maftools","owner":"PoisonAlien","description":"Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.","archived":false,"fork":false,"pushed_at":"2025-04-29T20:28:15.000Z","size":75849,"stargazers_count":462,"open_issues_count":16,"forks_count":222,"subscribers_count":21,"default_branch":"master","last_synced_at":"2025-05-11T20:03:14.362Z","etag":null,"topics":["bioinformatics","cancer-genome-atlas","cancer-genomics","genomics","maf-files","r","tcga"],"latest_commit_sha":null,"homepage":"http://bioconductor.org/packages/release/bioc/html/maftools.html","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PoisonAlien.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2016-01-06T08:15:28.000Z","updated_at":"2025-04-28T14:49:36.000Z","dependencies_parsed_at":"2023-01-24T12:46:10.930Z","dependency_job_id":"6728b157-49c6-40db-80e1-aad1acca3155","html_url":"https://github.com/PoisonAlien/maftools","commit_stats":{"total_commits":748,"total_committers":31,"mean_commits":"24.129032258064516","dds":"0.15374331550802134","last_synced_commit":"7c08a055dbea241804813c962992a4233b978bf8"},"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fmaftools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fmaftools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fmaftools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fmaftools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PoisonAlien","download_url":"https://codeload.github.com/PoisonAlien/maftools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254069914,"owners_count":22009558,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","cancer-genome-atlas","cancer-genomics","genomics","maf-files","r","tcga"],"created_at":"2024-10-03T20:07:31.597Z","updated_at":"2025-05-14T04:08:38.509Z","avatar_url":"https://github.com/PoisonAlien.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"vignettes/maftools_hex.svg\" align=\"left\" height=\"140\" /\u003e\u003c/a\u003e\n\n## maftools - An R package to summarize, analyze and visualize MAF files\n\n[![GitHub closed issues](https://img.shields.io/github/issues-closed-raw/poisonalien/maftools.svg)](https://github.com/poisonalien/maftools/issues)\n[![R-CMD-check](https://github.com/PoisonAlien/maftools/workflows/R-CMD-check/badge.svg)](https://github.com/PoisonAlien/maftools/actions)\n\n## Introduction\n\nmaftools 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](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/) as the only input file type.\n\n## Installation\n\n```{r}\n#Install from Bioconductor repository\nBiocManager::install(\"maftools\")\n\n#Install from GitHub repository\nBiocManager::install(\"PoisonAlien/maftools\")\n```\n\n## Getting started: Vignette and a case study\n\nA complete documentation of maftools using [TCGA LAML](https://www.nejm.org/doi/full/10.1056/nejmoa1301689) as a case study can be found [here](http://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html).\n\n\u003cp align=\"left\"\u003e\n\u003cimg src=\"https://user-images.githubusercontent.com/8164062/97981605-d8a59500-1dd2-11eb-9f5e-cc808f7b3f91.gif\" height=\"320\" height=\"400\"\u003e\n\u003c/p\u003e\n\n## Primary applications \n\nmaftools is extremely easy to use, starting with importing an [MAF](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/) 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:\n\n- [Cohort summarization using oncoplots](https://bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/oncoplots.html#08_Combining_everything)\n- [Identify co-occurring and mutually exclusive events](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#91_Somatic_Interactions)\n- [Clinical enrichment analysis](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#96_Clinical_enrichment_analysis)\n- [Detect cancer driver genes](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#92_Detecting_cancer_driver_genes_based_on_positional_clustering)\n- [Infer tumor heterogeneity](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#99_Tumor_heterogeneity_and_MATH_scores)\n- [Analyze known cancer signaling pathways](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#98_Oncogenic_Signaling_Pathways)\n- [De-novo somatic signature analysis with NMF](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#9103_Signature_analysis)\n- [Compare two cohorts to identify differentially mutated genes](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#95_Comparing_two_cohorts_(MAFs))\n- [Perform survival analysis and predict genesets associated with survival](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#942_Predict_genesets_associated_with_survival)\n- [Drug-gene interactions](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#97_Drug-Gene_Interactions)\n\nBesides 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.\n\n- [Generate personalized cancer report](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/cancer_hotspots.html) for known somatic [hotspots](https://www.cancerhotspots.org/)\n- [Sample mismatch and relatedness analysis](https://bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html#12_Sample_swap_identification)\n- [Copy number analysis](https://bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/cnv_analysis.html) with [ASCAT](https://github.com/VanLoo-lab/ascat) and [mosdepth](https://github.com/brentp/mosdepth)\n\nMoreover, analyzing all 33 TCGA cohorts along with the harmonized clinical data is a breeze. \n\n- A single command [tcgaLoad](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#13_TCGA_cohorts) will import the desired TCGA cohort thereby avoiding costly time spent on data mining from public databases. \n- Please refer to an associated software package [TCGAmutations](https://github.com/PoisonAlien/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.\n\n## Citation\n\n**_Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. 2018. Maftools: efficient and comprehensive analysis of somatic variants in cancer. [Genome Research](https://doi.org/10.1101/gr.239244.118). PMID: [30341162](https://www.ncbi.nlm.nih.gov/pubmed/?term=30341162)_**\n\n\n## Useful links\n\n| File Fomats                                                                                                        | Data portals                                                                                    | Annotation tools                                                                                                                       |\n|--------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------|\n| [Mutation Annotation Format](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/)                            | [TCGA](http://cancergenome.nih.gov)                                                             | [vcf2maf](https://github.com/mskcc/vcf2maf) - for converting your VCF files to MAF                                                     |\n| [Variant Call Format](https://en.wikipedia.org/wiki/Variant_Call_Format)                                           | [ICGC](https://docs.icgc.org/)                                                                  | [annovar2maf](https://github.com/PoisonAlien/annovar2maf) - for converting annovar output files to MAF                                 |\n| ICGC [Simple Somatic Mutation Format](https://docs.icgc.org/submission/guide/icgc-simple-somatic-mutation-format/) | [Broad Firehose](https://gdac.broadinstitute.org/)                                              | [bcftools csq](https://samtools.github.io/bcftools/howtos/csq-calling.html) - Rapid annotations of VCF files with variant consequences |\n|                                                                                                                    | [cBioPortal](https://www.cbioportal.org/)                                                       | [Annovar](https://annovar.openbioinformatics.org/en/latest/)                                                              |\n|                                                                                                                    | [PeCan](https://pecan.stjude.cloud/)                                                            | [Funcotator](https://gatk.broadinstitute.org/hc/en-us/articles/360037224432-Funcotator)                                                |\n|                                                                                                                    | [CIViC](https://civicdb.org/home) - Clinical interpretation of variants in cancer               |                                                                                                                                        |\n|                                                                                                                    | [DGIdb](http://www.dgidb.org/) - Information on drug-gene interactions and the druggable genome |                                                                                                                                        |\n\n\n## Useful packages/tools\n\nBelow are some more useful software packages for somatic variant analysis\n\n* [TRONCO](https://github.com/BIMIB-DISCo/TRONCO) - Repository of the TRanslational ONCOlogy library (R)\n* [dndscv](https://github.com/im3sanger/dndscv) - dN/dS methods to quantify selection in cancer and somatic evolution (R)\n* [cloneevol](https://github.com/hdng/clonevol) - Inferring and visualizing clonal evolution in multi-sample cancer sequencing (R)\n* [sigminer](https://github.com/ShixiangWang/sigminer) - Primarily for signature analysis and visualization in R. Supports `maftools` output (R)\n* [GenVisR](https://github.com/griffithlab/GenVisR) - Primarily for visualization (R)\n* [comut](https://github.com/vanallenlab/comut) - Primarily for visualization (Python)\n* [TCGAmutations](https://github.com/PoisonAlien/TCGAmutations) - pre-compiled curated somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project) that can be loaded into `maftools` (R)\n* [somaticfreq](\u003chttps://github.com/PoisonAlien/somaticfreq\u003e) - rapid genotyping of known somatic hotspot variants from the tumor BAM files. Generates a browsable/sharable HTML report. (C)\n\n***\n\n#### Powered By\n\n* [data.table](https://github.com/Rdatatable/data.table/wiki) at [warp speed](https://en.wikipedia.org/wiki/Warp_drive)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpoisonalien%2Fmaftools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpoisonalien%2Fmaftools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpoisonalien%2Fmaftools/lists"}