{"id":30019648,"url":"https://github.com/veupathdb/vdi-plugin-rnaseq","last_synced_at":"2025-09-13T01:43:54.362Z","repository":{"id":164172384,"uuid":"618507181","full_name":"VEuPathDB/vdi-plugin-rnaseq","owner":"VEuPathDB","description":null,"archived":false,"fork":false,"pushed_at":"2025-06-26T16:59:38.000Z","size":163,"stargazers_count":0,"open_issues_count":2,"forks_count":0,"subscribers_count":17,"default_branch":"main","last_synced_at":"2025-08-06T01:31:36.242Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"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/VEuPathDB.png","metadata":{"files":{"readme":"readme.adoc","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,"zenodo":null}},"created_at":"2023-03-24T16:06:09.000Z","updated_at":"2025-06-26T16:59:40.000Z","dependencies_parsed_at":"2024-04-29T20:27:53.209Z","dependency_job_id":"bce4aa27-f440-4ab7-98af-536304b7b9e2","html_url":"https://github.com/VEuPathDB/vdi-plugin-rnaseq","commit_stats":null,"previous_names":["veupathdb/vdi-plugin-rnaseq"],"tags_count":31,"template":false,"template_full_name":"VEuPathDB/vdi-plugin-example","purl":"pkg:github/VEuPathDB/vdi-plugin-rnaseq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fvdi-plugin-rnaseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fvdi-plugin-rnaseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fvdi-plugin-rnaseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fvdi-plugin-rnaseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VEuPathDB","download_url":"https://codeload.github.com/VEuPathDB/vdi-plugin-rnaseq/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2Fvdi-plugin-rnaseq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273088754,"owners_count":25043556,"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":"2025-09-01T02:00:09.058Z","response_time":120,"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":"2025-08-06T01:20:18.255Z","updated_at":"2025-09-01T07:32:53.029Z","avatar_url":"https://github.com/VEuPathDB.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"= VDI RNA Seq Handler\n:icons: font\n\nifdef::env-github[]\n:tip-caption: :bulb:\n:note-caption: :information_source:\n:important-caption: :heavy_exclamation_mark:\n:caution-caption: :fire:\n:warning-caption: :warning:\nendif::[]\n\nThis is the VDI Handler for RNA Seq datasets.  These datasets contain FPKM data in .txt files, and optionally bigwig files used for genome browser tracks.\n\nSee the https://github.com/VEuPathDB/vdi-handler-plugin-example[VDI Handler Example repo] for background.\n\nFor more details about the scripts themselves and their inputs and outputs see\nthe https://github.com/VEuPathDB/vdi-plugin-handler-server[VDI Plugin Handler Server]\nreadme.\n\nThe `import` script does its best to validate the dataset.  On the assumption that the dataset is provided by the VEuPathDB RNA Seq Exporter, we hope that it was constructed validly.  It is possible the validator will miss ways the dataset could go wrong.\n\nHere is a manifest file from a stranded dataset\n\n```\nSRR5260550.fastq-forward\tSRR5260550.fastq-forward.bw\tfirststrand\nSRR5260550.fastq-reverse\tSRR5260550.fastq-reverse.bw\tsecondstrand\nSRR5260551.fastq-forward\tSRR5260551.fastq-forward.bw\tfirststrand\nSRR5260551.fastq-reverse\tSRR5260551.fastq-reverse.bw\tsecondstrand\nSRR5260552.fastq-forward\tSRR5260552.fastq-forward.bw\tfirststrand\nSRR5260552.fastq-reverse\tSRR5260552.fastq-reverse.bw\tsecondstrand\nSRR5260550.fastq-one\tSRR5260550.fastq-one.txt\tsense\nSRR5260550.fastq-two\tSRR5260550.fastq-two.txt\tantisense\nSRR5260551.fastq-one\tSRR5260551.fastq-one.txt\tsense\nSRR5260551.fastq-two\tSRR5260551.fastq-two.txt\tantisense\nSRR5260552.fastq-one\tSRR5260552.fastq-one.txt\tsense\nSRR5260552.fastq-two\tSRR5260552.fastq-two.txt\tantisense\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fveupathdb%2Fvdi-plugin-rnaseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fveupathdb%2Fvdi-plugin-rnaseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fveupathdb%2Fvdi-plugin-rnaseq/lists"}