{"id":32111541,"url":"https://github.com/al2na/methylkit","last_synced_at":"2025-10-20T14:37:20.458Z","repository":{"id":12750941,"uuid":"15424141","full_name":"al2na/methylKit","owner":"al2na","description":"R package for DNA methylation analysis","archived":false,"fork":false,"pushed_at":"2025-09-07T15:24:22.000Z","size":19422,"stargazers_count":237,"open_issues_count":70,"forks_count":101,"subscribers_count":17,"default_branch":"master","last_synced_at":"2025-10-18T02:23:33.248Z","etag":null,"topics":["genome-biology","methylation","statistical-analysis","visualization"],"latest_commit_sha":null,"homepage":"https://bioconductor.org/packages/release/bioc/html/methylKit.html","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/al2na.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","contributing":null,"funding":null,"license":null,"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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2013-12-24T19:35:57.000Z","updated_at":"2025-10-04T13:55:25.000Z","dependencies_parsed_at":"2025-01-07T17:38:22.502Z","dependency_job_id":"dbb19188-3c29-4227-90e4-192760e669cc","html_url":"https://github.com/al2na/methylKit","commit_stats":{"total_commits":951,"total_committers":30,"mean_commits":31.7,"dds":0.7287066246056783,"last_synced_commit":"388770da40bde7d563224cc5d2259c2a7a6a2e08"},"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/al2na/methylKit","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/al2na%2FmethylKit","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/al2na%2FmethylKit/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/al2na%2FmethylKit/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/al2na%2FmethylKit/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/al2na","download_url":"https://codeload.github.com/al2na/methylKit/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/al2na%2FmethylKit/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280106127,"owners_count":26273107,"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","status":"online","status_checked_at":"2025-10-20T02:00:06.978Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["genome-biology","methylation","statistical-analysis","visualization"],"created_at":"2025-10-20T14:37:17.795Z","updated_at":"2025-10-20T14:37:20.452Z","avatar_url":"https://github.com/al2na.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n\n\u003ca name=\"logo\"/\u003e\n\u003cdiv align=\"center\"\u003e\n\u003cimg src=\"https://raw.githubusercontent.com/al2na/methylKit/master/inst/methylKit_logo.png\" alt=\"methylKit Logo\"  \u003e\u003c/img\u003e\n\u003c/a\u003e\n\u003c/div\u003e\n\nmethylKit \n========\n\nBuild Status \n\n|  |  | \n| - | - |\n| Github | [![Build Status](https://github.com/al2na/methylKit/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/al2na/methylKit/actions/workflows/check-standard.yaml) |\n| Bioc Release | [![Bioc release status](https://www.bioconductor.org/shields/build/release/bioc/methylKit.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/methylKit) | \nBioc Devel | [![Bioc devel status](https://www.bioconductor.org/shields/build/devel/bioc/methylKit.svg?text=esfes\u0026)](https://bioconductor.org/checkResults/devel/bioc-LATEST/methylKit) | \n\n\n[![GitHub R package version](https://img.shields.io/github/r-package/v/al2na/methylKit?label=version\u0026)](https://github.com/al2na/methylKit/blob/master/NEWS)\n[![codecov](https://codecov.io/github/al2na/methylKit/branch/master/graphs/badge.svg)](https://codecov.io/github/al2na/methylKit) \n\n# Introduction\n\n*methylKit* is an [R](http://en.wikipedia.org/wiki/R_%28programming_language%29) package \nfor DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The \npackage is designed to deal with sequencing data from \n[RRBS](http://www.nature.com/nprot/journal/v6/n4/abs/nprot.2010.190.html) and its variants,\nbut also target-capture methods such as [Agilent SureSelect \nmethyl-seq](http://www.halogenomics.com/sureselect/methyl-seq). \nIn addition, methylKit can \ndeal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also \nhandle whole-genome bisulfite sequencing data if proper input format is provided.\n\n## Current Features\n\n * Coverage statistics\n * Methylation statistics\n * Sample correlation and clustering\n * Differential methylation analysis \n * Feature annotation and accessor/coercion functions \n * Multiple visualization options  \n * Regional and tiling windows analysis\n * (Almost) proper [documentation](https://bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html)\n * Reading methylation calls directly from [Bismark(Bowtie/Bowtie2](http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/) alignment files\n * Batch effect control\n * Multithreading support (for faster differential methylation calculations) \n * Coercion to objects from Bioconductor package GenomicRanges\n * Reading methylation percentage data from generic text files\n\n\n\n\n\n## Staying up-to-date\n\nYou can subscribe to our googlegroups page to get the latest information about new releases and features (low-frequency, only updates are posted)\n\n- https://groups.google.com/forum/#!forum/methylkit\n\nTo ask questions please use methylKit_discussion forum\n\n- https://groups.google.com/forum/#!forum/methylkit_discussion\n\nYou can also check out the blogposts we make on using methylKit\n\n- http://zvfak.blogspot.de/search/label/methylKit\n\n-------\n\n## Installation\n\nin R console,\n```r\nlibrary(devtools)\ninstall_github(\"al2na/methylKit\", build_vignettes=FALSE, \n  repos=BiocManager::repositories(),\n  dependencies=TRUE)\n```\nif this doesn't work, you might need to add `type=\"source\"` argument.\n\n### Install the development version\n```r\nlibrary(devtools)\ninstall_github(\"al2na/methylKit\", build_vignettes=FALSE, \n  repos=BiocManager::repositories(),ref=\"development\",\n  dependencies=TRUE)\n```\nif this doesn't work, you might need to add `type=\"source\"` argument.\n\n\n-------\n\n# How to Use\n\nTypically, bisulfite converted reads are aligned to the genome and % methylation value per base is calculated by processing alignments. *`methylKit`* takes that  % methylation value per base information as input. Such input file may be obtained from [AMP pipeline](http://code.google.com/p/amp-errbs/) for aligning RRBS reads. A typical input file looks like this:\n\n```\nchrBase\tchr\tbase\tstrand\tcoverage\tfreqC\tfreqT\nchr21.9764539\tchr21\t9764539\tR\t12\t25.00\t75.00\nchr21.9764513\tchr21\t9764513\tR\t12\t0.00\t100.00\nchr21.9820622\tchr21\t9820622\tF\t13\t0.00\t100.00\nchr21.9837545\tchr21\t9837545\tF\t11\t0.00\t100.00\nchr21.9849022\tchr21\t9849022\tF\t124\t72.58\t27.42\nchr21.9853326\tchr21\t9853326\tF\t17\t70.59\t29.41\n\n```\n\n\n*`methylKit`* reads in those files and performs basic statistical analysis and annotation for differentially methylated regions/bases. Also a tab separated text file with a generic format can be read in, such as methylation ratio files from [BSMAP](http://code.google.com/p/bsmap/), see [here](http://zvfak.blogspot.com/2012/10/how-to-read-bsmap-methylation-ratio.html) for an example. Alternatively, `read.bismark` function can read SAM file(s) output by [Bismark](http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/)(using bowtie/bowtie2) aligner (the SAM file must be sorted based on chromosome and read start). The sorting must be done by unix sort or samtools, sorting using other tools may change the column order of the SAM file and that will cause an error. \n\nBelow, there are several options showing how to do basic analysis with *`methylKit`*.\n\n## Documentation ##\n * You can look at the vignette [here](https://bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html). This is the primary source of documentation. It includes detailed examples.\n * You can check out the [slides](https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/methylkit/methylKitTutorialSlides_2013.pdf ) for a tutorial at EpiWorkshop 2013. This works with older versions of methylKit, you may need to update the function names.\n * You can check out the [tutorial](https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/methylkit/methylKitTutorial_feb2012.pdf) prepared for  EpiWorkshop 2012. This works with older versions of methylKit, you may need to update the function names.\n* You can check out the [slides](https://www.slideshare.net/AlexanderGosdschan/eurobioc-2018-metyhlkit-overview) prepared for EuroBioc 2018. This also includes more recent features of methylKit  and is meant to give you a quick overview about what you can do with the package. \n\n\n\n\n\n\n## Downloading Annotation Files\nAnnotation files in BED format are needed for annotating your differentially methylated regions. You can download annotation files from UCSC table browser for your genome of interest. Go to  [http://genome.ucsc.edu/cgi-bin/hgGateway]. On the top menu click on \"tools\" then \"table browser\". Select your \"genome\" of interest and \"assembly\" of interest from the drop down menus. Make sure you select the correct genome and assembly. Selecting wrong genome and/or assembly will return unintelligible results in downstream analysis. \n\nFrom here on you can either download *gene annotation* or *CpG island annotation*.\n\n1. For gene annotation, select _\"Genes and Gene prediction tracks\"_ from the *\"group\"* drop-down menu. Following that, select _\"Refseq Genes\"_ from the *\"track\"* drop-down menu. Select _\"BED- browser extensible data\"_ for the *\"output format\"*. Click *\"get output\"* and on the following page click *\"get BED\"* without changing any options. save the output as a text file.\n2. For CpG island annotation, select _\"Regulation\"_ from the *\"group\"* drop-down menu. Following that, select _\"CpG islands\"_ from the *\"track\"* drop-down menu. Select _\"BED- browser extensible data\"_  for the *\"output format\"*. Click *\"get output\"* and on the following page click *\"get BED\"* without changing any options. save the output as a text file.\n\n\nIn addition, you can check this tutorial to learn how to download any track from UCSC in BED format (http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28)\n\n\n\n\n-------\n# R script for Genome Biology publication\nThe most recent version of the R script in the Genome Biology manuscript is [here](http://code.google.com/p/methylkit/downloads/list?q=label:AdditionalFile4 ).\n\n-------\n# Citing methylKit\nIf you used methylKit please cite:\n\n\n * Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E. Garrett-Bakelman, Maria E. Figueroa, Ari Melnick, Christopher E. Mason. _(2012)_. *\"[methylKit: A comprehensive R package for the analysis of genome-wide DNA methylation profiles.](http://genomebiology.com/2012/13/10/R87/)\"* _Genome Biology_ , 13:R87.\n\nIf you used flat-file objects or over-dispersion corrected tests please consider citing:\n\n* Wreczycka K, Gosdschan A, Yusuf D, Grüning B, Assenov Y, Akalin A. *\"[Strategies for analyzing bisulfite sequencing data.](https://linkinghub.elsevier.com/retrieve/pii/S0168-1656(17)31593-6)\"* J Biotechnol., 2017\n\nand also consider citing the following publication as a use-case with specific cutoffs:\n\n * Altuna Akalin, Francine E. Garrett-Bakelman, Matthias Kormaksson, Jennifer Busuttil, Lu Zhang, Irina Khrebtukova, Thomas A. Milne, Yongsheng Huang, Debabrata Biswas, Jay L. Hess, C. David Allis, Robert G. Roeder, Peter J. M. Valk, Bob Löwenberg, Ruud Delwel, Hugo F. Fernandez, Elisabeth Paietta, Martin S. Tallman, Gary P. Schroth, Christopher E. Mason, Ari Melnick, Maria E. Figueroa. _(2012)_. *\"[Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia.](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002781)\"* _PLoS Genetics_ 8(6).\n\n-------\n# Contact \u0026 Questions\ne-mail to [methylkit_discussion@googlegroups.com](mailto:methylkit_discussion@googlegroups.com ) or post a question using [the web interface](https://groups.google.com/forum/#!forum/methylkit_discussion).\n\nif you are going to submit bug reports or ask questions, please send sessionInfo() output from R console as well.\n\nQuestions are very welcome, although we suggest you read the paper, documentation(function help pages and the vignette) and [ blog entries](http://zvfak.blogspot.com/search/label/methylKit) first. The answer to your question might be there already.\n\n-------\n# Contribute to the development\nSee the [trello board](https://trello.com/b/k2kv1Od7/methylkit) for methylKit development. You can contribute to the methylKit development via github ([http://github.com/al2na/methylKit/]) by opening an issue and discussing what you want to contribute, we will guide you from there. In addition, you should:\n\n * Bump up the version in the DESCRIPTION file on the 3rd number. For example, the master branch has the version numbering as in \"X.Y.1\". If you make a change to master branch you should bump up the version in the DESCRIPTION file to \"X.Y.2\".\n\n * Add your changes to the NEWS file as well under the correct version and appropriate section. Attribute the changes to yourself, such as \"Contributed by X\"\n \nLicense\n---------\nArtistic License/GPL\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fal2na%2Fmethylkit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fal2na%2Fmethylkit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fal2na%2Fmethylkit/lists"}