{"id":17223302,"url":"https://github.com/slowkow/centipede.tutorial","last_synced_at":"2025-04-14T00:22:07.565Z","repository":{"id":34559273,"uuid":"38504710","full_name":"slowkow/CENTIPEDE.tutorial","owner":"slowkow","description":":bug: How to use CENTIPEDE to determine if a transcription factor is bound.","archived":false,"fork":false,"pushed_at":"2018-03-18T14:39:30.000Z","size":3946,"stargazers_count":26,"open_issues_count":5,"forks_count":13,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-27T14:21:53.541Z","etag":null,"topics":["bioinformatics","dnase-seq","enrichment","rstats","transcription-factors","tutorial"],"latest_commit_sha":null,"homepage":"https://slowkow.github.io/CENTIPEDE.tutorial","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/slowkow.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":"2015-07-03T17:57:24.000Z","updated_at":"2024-12-03T03:26:24.000Z","dependencies_parsed_at":"2022-09-04T05:41:59.477Z","dependency_job_id":null,"html_url":"https://github.com/slowkow/CENTIPEDE.tutorial","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/slowkow%2FCENTIPEDE.tutorial","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/slowkow%2FCENTIPEDE.tutorial/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/slowkow%2FCENTIPEDE.tutorial/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/slowkow%2FCENTIPEDE.tutorial/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/slowkow","download_url":"https://codeload.github.com/slowkow/CENTIPEDE.tutorial/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248800048,"owners_count":21163404,"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","dnase-seq","enrichment","rstats","transcription-factors","tutorial"],"created_at":"2024-10-15T04:08:03.438Z","updated_at":"2025-04-14T00:22:07.537Z","avatar_url":"https://github.com/slowkow.png","language":"R","readme":"# CENTIPEDE Tutorial\n\n\u003e CENTIPEDE fits a bayesian hierarchical mixture model to learn TF-specific\n\u003e distribution of experimental data on a particular cell-type for a set of\n\u003e candidate binding sites described by a motif.\n\nThis is a practical tutorial for running [CENTIPEDE] with [DNase-Seq] data. It\nexplains how to prepare the data and how to run the analysis. The goal is to\npredict if a putative transcription factor binding site is actually bound or\nnot. For details about the statistical models underlying the methods, please\nsee ([Pique-Regi, et al. 2011][1]).\n\n[CENTIPEDE]: http://centipede.uchicago.edu/ \n[DNase-Seq]: https://en.wikipedia.org/wiki/DNase-Seq\n[1]: http://genome.cshlp.org/content/21/3/447\n\nRead the tutorial online or download the PDF:\n\n- \u003chttps://slowkow.github.io/CENTIPEDE.tutorial\u003e\n- [centipede-tutorial.pdf][2]\n\n[2]: https://github.com/slowkow/CENTIPEDE.tutorial/raw/master/vignettes/centipede-tutorial.pdf\n\nThis repository has functions to ease the use of CENTIPEDE:\n\n- `centipede_data()` converts data to the format required for CENTIPEDE.\n- `parse_region()` parses a string like \"chr1:123-456\".\n- `read_bedGraph()` reads a bedGraph file with 4 columns: chrom, start, end, score.\n- `read_fimo()` reads a text file output by FIMO and selects sites that meet a\n  significance threshold.\n\nI also provide example data that you can use to follow the tutorial:\n\n- `cen` is a list with two items:\n  - `cen$mat` is a matrix of read-start counts for 3,337 genomic regions.\n  - `cen$regions` is a dataframe describing those regions.\n- `site_cons` is a vector with mean conservation scores for the 3,337 regions,\n  computed across 100 vertebrates.\n\n# Installation\n\nInstall CENTIPEDE by running this in your shell (not within an R session):\n\n```bash\nwget http://download.r-forge.r-project.org/src/contrib/CENTIPEDE_1.2.tar.gz\nR CMD INSTALL CENTIPEDE_1.2.tar.gz\n```\n\nNext, install the tutorial package:\n\n```r\n# This command didn't work for me.\n# install.packages(\"CENTIPEDE\", repos=\"http://R-Forge.R-project.org\")\n\ninstall.packages(\"devtools\")\ndevtools::install_github(\"slowkow/CENTIPEDE.tutorial\")\n```\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fslowkow%2Fcentipede.tutorial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fslowkow%2Fcentipede.tutorial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fslowkow%2Fcentipede.tutorial/lists"}