{"id":21578153,"url":"https://github.com/hanjunlee21/panchip","last_synced_at":"2026-03-08T08:33:58.429Z","repository":{"id":57450368,"uuid":"424777555","full_name":"hanjunlee21/PanChIP","owner":"hanjunlee21","description":"Pan-ChIP-seq Analysis of Peak Sets","archived":false,"fork":false,"pushed_at":"2022-08-22T17:21:10.000Z","size":6255,"stargazers_count":0,"open_issues_count":1,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-23T04:38:37.084Z","etag":null,"topics":["bedfile","chip-seq"],"latest_commit_sha":null,"homepage":"","language":"Python","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/hanjunlee21.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-11-05T00:09:00.000Z","updated_at":"2022-05-07T23:06:25.000Z","dependencies_parsed_at":"2022-08-25T23:00:28.538Z","dependency_job_id":null,"html_url":"https://github.com/hanjunlee21/PanChIP","commit_stats":null,"previous_names":[],"tags_count":39,"template":false,"template_full_name":null,"purl":"pkg:github/hanjunlee21/PanChIP","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hanjunlee21%2FPanChIP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hanjunlee21%2FPanChIP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hanjunlee21%2FPanChIP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hanjunlee21%2FPanChIP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/hanjunlee21","download_url":"https://codeload.github.com/hanjunlee21/PanChIP/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hanjunlee21%2FPanChIP/sbom","scorecard":{"id":454531,"data":{"date":"2025-08-11","repo":{"name":"github.com/hanjunlee21/PanChIP","commit":"d0f51d1dfab8b95868888fa4bc6a48d127c0b1ea"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":3,"checks":[{"name":"SAST","score":0,"reason":"no SAST tool detected","details":["Warn: no pull requests merged into dev branch"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}},{"name":"Token-Permissions","score":-1,"reason":"No tokens found","details":null,"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Code-Review","score":0,"reason":"Found 0/30 approved changesets -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Dangerous-Workflow","score":-1,"reason":"no workflows found","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Pinned-Dependencies","score":-1,"reason":"no dependencies found","details":null,"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"Vulnerabilities","score":10,"reason":"0 existing vulnerabilities detected","details":null,"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE.txt:0","Info: FSF or OSI recognized license: MIT License: LICENSE.txt:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'main'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}}]},"last_synced_at":"2025-08-19T09:12:22.478Z","repository_id":57450368,"created_at":"2025-08-19T09:12:22.478Z","updated_at":"2025-08-19T09:12:22.478Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279001982,"owners_count":26083259,"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":"2025-10-09T02:00:07.460Z","response_time":59,"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":["bedfile","chip-seq"],"created_at":"2024-11-24T13:09:46.612Z","updated_at":"2026-03-08T08:33:58.421Z","avatar_url":"https://github.com/hanjunlee21.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PanChIP\n**Pan-ChIP-seq Analysis of Protein Colocalization Using Peak Sets**\n\n[![PyPI version](https://badge.fury.io/py/PanChIP.svg)](https://badge.fury.io/py/PanChIP)\n[![DOI](https://zenodo.org/badge/424777555.svg)](https://zenodo.org/badge/latestdoi/424777555)\n\n\u003cbr/\u003e\n\nThe current version of PanChIP supports the hg38 genome assembly.\n\n## Prerequisites\nPython 3, BEDTools\n\n## Installation\n**Installation by PyPI**\n```shell\npip3 install panchip\n```\n\n**Installation by Bioconda**\n```shell\nconda install bioconda::panchip\n```\n\n## Input\n```shell\nPanChIP Analysis: a directory with only 6-column BED files\nPanChIP Filter: a 6-column BED file\n\nWe recommend most PanChIP users to utilize BED files with constant non-zero fifth column values (e.g., 1, 500, 1000).\n```\n\n## Usage\n\n### panchip \u003ccommand\u003e [options]\n\n```shell\nCommands:\n    init            Initialization of the PanChIP library\n    analysis        Analysis of a list peak sets\n    filter          Filtering library for quality control\nRun panchip \u003ccommand\u003e -h for help on a specific command.\n\nPanChIP: Pan-ChIP-seq Analysis of Peak Sets\n\npositional arguments:\n  command     Subcommand to run\n\noptional arguments:\n  -h, --help  show this help message and exit\n  --version   show program's version number and exit\n```\n\n### panchip init [-h] library_directory\n\n```shell\n\nInitialization of the PanChIP library\n\npositional arguments:\n  library_directory  Directory wherein PanChIP library will be stored. \u003e 13.6\n                     GB of storage required.\n\noptional arguments:\n  -h, --help         show this help message and exit\n```\n\n### panchip analysis [-h] [-t THREADS] [-r REPEATS] library_directory input_directory output_directory\n\n```shell\n\nAnalysis of a list peak sets\n\npositional arguments:\n  library_directory  Directory wherein PanChIP library was stored.\n  input_directory    Input directory wherein peak sets in the format of .bed\n                     files are located.\n                     (.bed6 format with numeric scores in 5th column required)\n  output_directory   Output directory wherein output files will be stored.\n\noptional arguments:\n  -h, --help         show this help message and exit\n  -t THREADS         Number of threads to use. (default: 1)\n  -r REPEATS         Number of repeats to perform. (default: 1)\n```\n\n### panchip filter [-h] [-t THREADS] library_directory input_file output_directory\n\n```shell\n\nFiltering library for quality control\n\npositional arguments:\n  library_directory  Directory wherein PanChIP library was stored.\n  input_file         Path to the input .bed file.\n                     (.bed6 format with numeric scores in 5th column required)\n  output_directory   Output directory wherein output files will be stored.\n\noptional arguments:\n  -h, --help         show this help message and exit\n  -t THREADS         Number of threads to use. (default: 1)\n```\n\n## Primary Citation\n\nPlease cite the original PanChIP paper for works that utilized the PanChIP software.\n\n- **Sanidas I, Lee H, Rumde PH, Boulay G, Morris R, Golczer G, Stanzione M, Hajizadeh S, Zhong J, Ryan MB, Corcoran RB, Drapkin BJ, Rivera MN, Dyson NJ, and Lawrence MS. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci, and is redistributed by cell cycle progression. _Molecular Cell_ 82.18 (2022).**\n\n## Extended Citation\n\nThe development of PanChIP was possible thanks to many groundbreaking works of fellow researchers. We highly recommend users to cite the Cistrome Data Browser as well.\n\n- **Zheng R, Wan C, Mei S, Qin Q, Wu Q, Sun H, Chen C-H, Brown M, Zhang X, Meyer CA, and Liu XS. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. _Nucleic Acids Research_ 47.D1, D729–D735 (2019).**\n\nWhile the design of PanChIP is different from that of BART, we suggest users to also try out the BART software. PanChIP measures the overlap between peak sets, while BART assesses the predictability of profiles based on the library.\n\n- **Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, and Zang C. BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. _Bioinformatics_ 34.16, 2867–2869 (2018).**\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhanjunlee21%2Fpanchip","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhanjunlee21%2Fpanchip","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhanjunlee21%2Fpanchip/lists"}