{"id":18813201,"url":"https://github.com/nellore/region_matrix","last_synced_at":"2026-01-12T08:30:17.251Z","repository":{"id":151483258,"uuid":"64560400","full_name":"nellore/region_matrix","owner":"nellore","description":"Tool for writing matrix of AUCs of indexed BAMs in regions specified by BED","archived":false,"fork":false,"pushed_at":"2016-07-30T19:57:10.000Z","size":28,"stargazers_count":1,"open_issues_count":1,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-12-30T00:24:49.506Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/nellore.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}},"created_at":"2016-07-30T19:17:07.000Z","updated_at":"2019-04-16T02:01:40.000Z","dependencies_parsed_at":null,"dependency_job_id":"edd34b0c-c827-4809-a787-dca3a8dacbcc","html_url":"https://github.com/nellore/region_matrix","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nellore%2Fregion_matrix","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nellore%2Fregion_matrix/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nellore%2Fregion_matrix/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nellore%2Fregion_matrix/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nellore","download_url":"https://codeload.github.com/nellore/region_matrix/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239748297,"owners_count":19690237,"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":[],"created_at":"2024-11-07T23:36:43.326Z","updated_at":"2025-02-19T23:18:02.887Z","avatar_url":"https://github.com/nellore.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Region matrix\nis a tool for writing the matrix of areas-under-the-curve (AUCs) of indexed BAMs in regions specified by a BED file. An AUC is the sum of the number of reads aligning across every base of the region. Only primary alignments in each BAM file are considered. When specifying regions in the BED file, remember that its coordinates are 0-based and half-open: the start coordinate is included in the region, while the end coordinate is excluded from the region.\n\nRequires Python 2.x and https://github.com/Ensembl/WiggleTools.\n\n## Usage\n\n```\npython region_matrix.py --regions \u003c3-column COORDINATE-SORTED BED file specifying regions\u003e \\\n                        [--bams \u003cspace-separated list of BAM files\u003e OR --bam-manifest \u003cpath to BAM manifest file] \\\n                        --wiggletools \u003cpath to wiggletools executable\u003e \\\n                        -p \u003cmax number of wiggletools processes to run at once\u003e\n```\n\n## Specifying BAMs\n\nBAMs may be specified as a space-separated list of paths after `--bams` or as the path to a BAM manifest file as the argument of `--bam-manifest`. Each line of the BAM manifest file takes the form\n```\n\u003cpath to indexed BAM\u003e\u003cTAB\u003e\u003csample name\u003e\n```\n. If BAMs are specified as the argument of `--bams`, sample names are taken to be their paths.\n\n## Output\n\nTable whose `(i, j)`th entry is the AUC of the `i`th sample in the `j`th region. Output is written to stdout; rows are labeled by sample, and columns are labeled by region.\n\n## License\n\nMIT. See `LICENSE` for details.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnellore%2Fregion_matrix","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnellore%2Fregion_matrix","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnellore%2Fregion_matrix/lists"}