{"id":45341959,"url":"https://github.com/kdkorthauer/dmrseq","last_synced_at":"2026-02-21T10:33:09.056Z","repository":{"id":49375276,"uuid":"97278089","full_name":"kdkorthauer/dmrseq","owner":"kdkorthauer","description":"R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing","archived":false,"fork":false,"pushed_at":"2025-05-09T17:38:40.000Z","size":24024,"stargazers_count":58,"open_issues_count":9,"forks_count":14,"subscribers_count":9,"default_branch":"devel","last_synced_at":"2025-05-09T18:35:20.871Z","etag":null,"topics":["bioconductor","bisulfite-sequencing","dmr","epigenetics","inference","methylation"],"latest_commit_sha":null,"homepage":"","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/kdkorthauer.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":"2017-07-14T22:48:24.000Z","updated_at":"2025-05-09T17:38:44.000Z","dependencies_parsed_at":"2022-08-25T04:21:03.667Z","dependency_job_id":"82d0fd97-2d72-48dd-92a3-48f72a27c540","html_url":"https://github.com/kdkorthauer/dmrseq","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/kdkorthauer/dmrseq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kdkorthauer%2Fdmrseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kdkorthauer%2Fdmrseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kdkorthauer%2Fdmrseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kdkorthauer%2Fdmrseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kdkorthauer","download_url":"https://codeload.github.com/kdkorthauer/dmrseq/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kdkorthauer%2Fdmrseq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29679049,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-21T09:33:50.764Z","status":"ssl_error","status_checked_at":"2026-02-21T09:33:19.949Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bioconductor","bisulfite-sequencing","dmr","epigenetics","inference","methylation"],"created_at":"2026-02-21T10:33:08.921Z","updated_at":"2026-02-21T10:33:09.049Z","avatar_url":"https://github.com/kdkorthauer.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# dmrseq: Inference for differentially methylated regions (DMRs) from bisulfite sequencing\n\nA central question in the analysis of bisulfite sequencing data \nis to detect regions (collections of \nneighboring CpGs) with systematic differences between conditions, \nas compared to within-condition variability. These so-called *Differentially\nMethylated Regions* (DMRs) are thought to be more informative than single CpGs \nin terms of of biological function. \n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"/inst/sticker/dmrseq.png\" height=\"300\"/\u003e\n\u003c/p\u003e\n\nThe package **dmrseq** \nprovides a rigorous permutation-based approach to\ndetect and perform inference for differential methylation by use of \ngeneralized least squares models that account for inter-individual and \ninter-CpG variability to generate region-level statistics that can be\ncomparable across the genome. The framework performs well even\non samples as small as two per group. \n\n## Installation\n\n**dmrseq** is available on \n[Bioconductor](https://bioconductor.org/packages/dmrseq). You can install\nit with R version 3.5.0 or higher with the following commands:\n\n```\ninstall.packages(\"BiocManager\")\nBiocManager::install(\"dmrseq\")\n```\n\n## Getting started\n\nSee the vignette for information on how to use the package to perform\ntypical methylation analysis workflows.\n\n## Learn more\n\nMore details of the **dmrseq** framework can be found in the manuscript\n\n\u003e Korthauer, K., Chakraborty, S., Benjamini, Y., and Irizarry, R.A.\n\u003e Detection and accurate False Discovery Rate control of differentially \nmethylated regions from Whole Genome Bisulfite Sequencing\n\u003e *Biostatistics*, 2018 (in press).\n\u003e [BioRxiv:10.1101/183210](http://www.biorxiv.org/content/early/2017/08/31/183210)\n\n\n## License/Copyright\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) \nThis package is made available under an MIT license.  \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkdkorthauer%2Fdmrseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkdkorthauer%2Fdmrseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkdkorthauer%2Fdmrseq/lists"}