{"id":18670009,"url":"https://github.com/blahah/dexperimentr","last_synced_at":"2025-11-06T18:30:33.507Z","repository":{"id":13382285,"uuid":"16070286","full_name":"blahah/dexperimentr","owner":"blahah","description":"Differential expression experiment workflows","archived":false,"fork":false,"pushed_at":"2019-07-10T10:50:37.000Z","size":60,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-12-27T19:13:31.588Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","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/blahah.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}},"created_at":"2014-01-20T12:39:29.000Z","updated_at":"2015-02-10T14:03:21.000Z","dependencies_parsed_at":"2022-09-15T19:20:54.679Z","dependency_job_id":null,"html_url":"https://github.com/blahah/dexperimentr","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/blahah%2Fdexperimentr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fdexperimentr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fdexperimentr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fdexperimentr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/blahah","download_url":"https://codeload.github.com/blahah/dexperimentr/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239500975,"owners_count":19649367,"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":"2024-11-07T08:49:29.690Z","updated_at":"2025-11-06T18:30:33.469Z","avatar_url":"https://github.com/blahah.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"dexperimentr\n============\n\ndexperimentr is a collection of tools for automating best-practise RNAseq differential expression workflows.\n\n**Warning!** This is pre-release software. Please don't cry if it doesn't work. Check back soon for the first release.\n\n\n## Usage\n\n**!! WARNING !!** these instructions will eventually be true... but they're not yet. At the moment, this is more of a design-by-help document.\n\nTo run the entire workflow, you need the following:\n\n1. your count data as a dataframe, samples as named columns and genes/transcripts as named rows\n2. the path to your annotation file, which is a TSV with the first column being gene/transcript identifiers, and subsequent columns containing information about those genes that you want to include in the output\n3. Your long-form GO term file, which is a TSV with columns: go.id, id, term, ontology, definition (see below)\n\nThen you just run the pipeline:\n\n```R\nlibrary(dexperimentr)\nrun_DE_workflow(counts, annotation, gene_ontology)\n```\n\nAn HTML report, `report.html`, will be generated with a log of the process and diagnostic plots and guidance to help you interpret your data.\n\nIn addition, the following directories will be created and populated:\n\n- `count_qc/`: Basic quality control information about your count data\n- `de_data/`: Expression data, differential expression probabilities and expression patterns\n- `de_qc/`: Quality control information about the differential expression experiment\n- `functional_analysis/`: Gene Ontology functional category enrichment analysis data and plots\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fblahah%2Fdexperimentr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fblahah%2Fdexperimentr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fblahah%2Fdexperimentr/lists"}