{"id":32563023,"url":"https://github.com/smithlabcode/cread","last_synced_at":"2025-10-29T02:56:20.375Z","repository":{"id":209384509,"uuid":"246170614","full_name":"smithlabcode/cread","owner":"smithlabcode","description":"Software tools for regulatory sequence analysis","archived":false,"fork":false,"pushed_at":"2023-11-29T22:06:21.000Z","size":369,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-04-01T00:29:55.507Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/smithlabcode.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}},"created_at":"2020-03-10T00:22:24.000Z","updated_at":"2023-11-27T01:54:06.000Z","dependencies_parsed_at":"2023-11-27T03:41:28.544Z","dependency_job_id":"b5754a3c-b457-423d-a617-181d6b319b0b","html_url":"https://github.com/smithlabcode/cread","commit_stats":null,"previous_names":["smithlabcode/cread"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/smithlabcode/cread","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fcread","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fcread/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fcread/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fcread/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/smithlabcode","download_url":"https://codeload.github.com/smithlabcode/cread/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fcread/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281549786,"owners_count":26520515,"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":"2025-10-29T02:00:06.901Z","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":[],"created_at":"2025-10-29T02:56:08.146Z","updated_at":"2025-10-29T02:56:20.370Z","avatar_url":"https://github.com/smithlabcode.png","language":"C++","readme":"# cread\n\nSoftware tools for regulatory sequence analysis\n\nCREAD: Comprehensive Regulatory Element Analysis and Discovery. The\nCREAD software package is a computational pipeline for understanding\nhow DNA and RNA elements participate in regulating gene expression.\nCREAD uses Pattern-Feature-Model framework for setting up analyses\nwith machine learning and pattern visualization to identify motifs\ninvolved in transcriptional regulation. CREAD also includes code\nlibraries to facilitate implementation of new tools.\n\nBuilding and Installing\n=======================\n\nThis software has been designed to run in a UNIX-like environment.\n\n* Step 1\n\n  This software package requires a functioning installation of the GNU\n  Scientific Library (GSL). If you don't already have this installed,\n  you can download it [here](http://www.gnu.org/software/gsl/). You can\n  also get it from apt, conda or brew.\n\n  If GSL is not installed in the default path,\n  ```console\n  export CPATH=/path_to_my_gsl/include\n  export LIBRARY_PATH=/path_to_my_gsl/lib\n  ```\n  will add search paths for compiling and linking.\n\n  You will also need to clone this repo recursively to get the source\n  with submodules:\n  ```console\n  git clone --recursive https://github.com/smithlabcode/cread.git\n  ```\n\n* Step 2\n\n  To build the binaries type the following from the root of the\n  source tree:\n  ```console\n  make\n  make install\n  ```\n  This will create all of the binaries and then create a `bin`\n  directory, in the current directory, containing all the binaries.\n\nContacts and Bug Reports\n========================\n\nAndrew D. Smith\nandrewds@usc.edu\n\nCopyright and License Information\n=================================\n\nCopyright (C) 2005-2023\nAndrew D. Smith\n\nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\nGNU General Public License for more details.\n\nYou should have received a copy of the GNU General Public License\nalong with this program.  If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Fcread","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmithlabcode%2Fcread","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Fcread/lists"}