{"id":13681216,"url":"https://github.com/omarwagih/rmotifx","last_synced_at":"2026-03-03T20:07:33.490Z","repository":{"id":23027803,"uuid":"26380475","full_name":"omarwagih/rmotifx","owner":"omarwagih","description":"Discovery of biological sequence motifs in R","archived":false,"fork":false,"pushed_at":"2018-12-20T07:08:25.000Z","size":634,"stargazers_count":28,"open_issues_count":5,"forks_count":12,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-10-29T08:23:54.934Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/omarwagih.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-11-09T01:10:34.000Z","updated_at":"2025-10-13T16:32:07.000Z","dependencies_parsed_at":"2022-08-21T18:50:16.431Z","dependency_job_id":null,"html_url":"https://github.com/omarwagih/rmotifx","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/omarwagih/rmotifx","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/omarwagih%2Frmotifx","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/omarwagih%2Frmotifx/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/omarwagih%2Frmotifx/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/omarwagih%2Frmotifx/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/omarwagih","download_url":"https://codeload.github.com/omarwagih/rmotifx/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/omarwagih%2Frmotifx/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30057849,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-03T18:21:05.932Z","status":"ssl_error","status_checked_at":"2026-03-03T18:20:59.341Z","response_time":61,"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":[],"created_at":"2024-08-02T13:01:27.950Z","updated_at":"2026-03-03T20:07:33.451Z","avatar_url":"https://github.com/omarwagih.png","language":"R","funding_links":[],"categories":["8. Kinase Motif/Activity Analysis"],"sub_categories":["Table of Contents"],"readme":"\n[![rmotifx](https://rawgit.com/omarwagih/rmotifx/master/inst/extdata/rmotifx-logo.svg)](https://github.com/omarwagih/rmotifx)\n\n## Introduction\nThis package contains a useable implementation the motif-x tool in the R programming language. motif-x (short for motif extractor) is a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background. For more information, please refer to the original [motif-x resource](http://motif-x.med.harvard.edu/). Please note that the current implementation only supports sequences with a fixed length (i.e. pre-aligned) and have a fixed central residue. For example, phosphorylation sites. \n\n## How to install?\nThe motif-x R package can be directly installed from github. First, ensure the `devotools` package is installed:\n\n```splus\ninstall.packages('devtools')\n```\n\nThen install rmotifx:\n\n```splus\nrequire(devtools)\ninstall_github('omarwagih/rmotifx')\n```\n\n## How to use?\nTo get started, fire up the motif-x package:\n\n```splus\nrequire(rmotifx)\n```\n\nThe package contains the function `motifx` which does everything. For a simple run, you will need a foreground and background set of sequences. \n\nWe can go ahead and use the sample data provided with the package: \n\n```splus\n# Get paths to sample files\nfg.path = system.file(\"extdata\", \"fg-data-ck2.txt\", package = \"rmotifx\")\nbg.path = system.file(\"extdata\", \"bg-data-serine.txt\", package = \"rmotifx\")\n\n# Read in sequences\nfg.seqs = readLines(fg.path)\nbg.seqs = readLines(bg.path)\n\n# You can take a look at the format of the sample data\nhead(fg.seqs)\nhead(bg.seqs)\n```\n\nHere, the foreground data represents phosphorylation binding sites of Casein Kinase 2. The negative data represents 10,000 random serine-centered sites.\n\nTo start the program, run the following:\n\n```splus\nmot = motifx(fg.seqs, bg.seqs, central.res = 'S', min.seqs = 20, pval.cutoff = 1e-6)\nprint(mot)\n```\n\nThe results returned should have the following format:\n\n```\n| motif           | score            | fg.matches | fg.size | bg.matches | bg.size | fold.increase    |\n|-----------------|------------------|------------|---------|------------|---------|------------------|\n| .......SD.E.... | 615.305311137178 | 57         | 399     | 23         | 6039    | 37.5093167701863 |\n| .......S..EE... | 318.377804126939 | 37         | 342     | 37         | 6016    | 17.5906432748538 |\n| .......SD.D.... | 615.305311137178 | 39         | 305     | 12         | 5979    | 63.7106557377049 |\n| .......SE.E.... | 314.760503514246 | 24         | 266     | 32         | 5967    | 16.8242481203008 |\n| .......S..E.... | 307.652655568589 | 56         | 242     | 325        | 5935    | 4.22581055308328 |\n| .......SE.D.... | 315.866504156853 | 21         | 186     | 26         | 5610    | 24.3610421836228 |\n| .......S..D.... | 10.915342261675  | 30         | 165     | 233        | 5584    | 4.35739367928209 |\n| .......SD...... | 9.3715112092424  | 25         | 135     | 224        | 5351    | 4.42377645502645 |\n| .......S.E..... | 7.27014238663954 | 25         | 110     | 342        | 5127    | 3.40709728867624 |\n```\n\nIt's that easy!\n\nFor detailed explanations of all parameters and output, check out the documentation by typing `?motifx`. You can also refer to the original motif-x [resource](http://motif-x.med.harvard.edu/motif-x.html) or [paper](http://motif-x.med.harvard.edu/publications/Chou_Schwartz_motif-x_CPBI_2011.pdf). \n\n\n## Citation\nIf you use rmotifx please do cite the following paper:\n\n\nWagih O, Sugiyama N, Ishihama Y, Beltrao P. (2015) Uncovering phosphorylation-based specificities through functional interaction networks (2015). *Mol. Cell. Proteomics* [PUBMED](http://www.ncbi.nlm.nih.gov/pubmed/26572964)\n\n## Todo\n\n- Add support for degenerate motifs\n- Add support for DNA sequences. Currently, only protein supported.\n- Allow motif discovery in non-centered k-mers\n\n## Feedback\nIf you have any feedback or suggestions, please drop me a line at (wagih(at)ebi.ac.uk) or open an issue on github.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fomarwagih%2Frmotifx","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fomarwagih%2Frmotifx","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fomarwagih%2Frmotifx/lists"}