{"id":23768569,"url":"https://github.com/nci-gdc/htseq-tool","last_synced_at":"2026-03-27T02:17:59.270Z","repository":{"id":37637346,"uuid":"49224066","full_name":"NCI-GDC/htseq-tool","owner":"NCI-GDC","description":"Utility scripts for processing HTSeq counts data","archived":false,"fork":false,"pushed_at":"2023-03-29T19:17:02.000Z","size":383,"stargazers_count":3,"open_issues_count":1,"forks_count":1,"subscribers_count":9,"default_branch":"master","last_synced_at":"2025-09-05T13:51:20.268Z","etag":null,"topics":["bioinformatics","docker","workflow-tool"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NCI-GDC.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","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":"2016-01-07T18:59:27.000Z","updated_at":"2024-02-18T06:47:09.000Z","dependencies_parsed_at":"2022-08-18T16:50:42.527Z","dependency_job_id":"c5bf66ee-1051-48f3-a60f-f1a90e72c7bd","html_url":"https://github.com/NCI-GDC/htseq-tool","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/NCI-GDC/htseq-tool","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fhtseq-tool","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fhtseq-tool/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fhtseq-tool/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fhtseq-tool/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NCI-GDC","download_url":"https://codeload.github.com/NCI-GDC/htseq-tool/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fhtseq-tool/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31009858,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-27T01:56:05.093Z","status":"online","status_checked_at":"2026-03-27T02:00:08.055Z","response_time":164,"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":["bioinformatics","docker","workflow-tool"],"created_at":"2025-01-01T01:37:35.762Z","updated_at":"2026-03-27T02:17:59.252Z","avatar_url":"https://github.com/NCI-GDC.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GDC Base Template\n![Version badge](https://img.shields.io/badge/htslib-1.8-\u003cCOLOR\u003e.svg)\n![Version badge](https://img.shields.io/badge/samtools-1.8-\u003cCOLOR\u003e.svg)\n![Version badge](https://img.shields.io/badge/HTSeq-0.6.1p1-\u003cCOLOR\u003e.svg)\n\nContains dockerfile and HTSeq utility tools for running the GDC HTSeq\nexpression quantification workflows. See https://github.com/NCI-GDC/htseq-cwl\nfor more information about the GDC workflow associated with this.\n\n## Usage\n\n### `gene_lengths`\n\nGenerate the gene exon lengths from GTF for use in normalization.\n\n```\nusage: htseq-tools gene_lengths [-h] --gtf_file GTF_FILE --out_file OUT_FILE\n\nExtract gene exon lengths from GTF\n\noptional arguments:\n  -h, --help           show this help message and exit\n  --gtf_file GTF_FILE  GTF file used for htseq count\n  --out_file OUT_FILE  Output TSV file to write to\n```\n\n### `merge_counts`\n\nWhen an aliquot has a mixture of paired- and single-end, this will\nmerge the counts to a single file.\n\n```\nusage: htseq-tools merge_counts [-h] --htseq_counts HTSEQ_COUNTS --out_file\n                                OUT_FILE\n\nMerge PE and SE counts from HTseq\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --htseq_counts HTSEQ_COUNTS\n                        HTSeq count file. Use multiple times\n  --out_file OUT_FILE   Output TSV file to write to\n```\n\n### `fpkm`\n\nNormalize the raw counts using the FPKM and FPKM-UQ methods.\n\n```\nusage: htseq-tools fpkm [-h] --aggregate_length_file AGGREGATE_LENGTH_FILE\n                        --htseq_counts HTSEQ_COUNTS --output_prefix\n                        OUTPUT_PREFIX\n\nGet FPKM and FPKM-UQ\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --aggregate_length_file AGGREGATE_LENGTH_FILE\n                        Aggregate length TSV\n  --htseq_counts HTSEQ_COUNTS\n                        HTSeq counts txt file\n  --output_prefix OUTPUT_PREFIX\n                        The output prefix to use.\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnci-gdc%2Fhtseq-tool","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnci-gdc%2Fhtseq-tool","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnci-gdc%2Fhtseq-tool/lists"}