{"id":20425021,"url":"https://github.com/databio/deseqpackager","last_synced_at":"2025-07-20T02:36:47.704Z","repository":{"id":86287784,"uuid":"111734108","full_name":"databio/DESeqPackager","owner":"databio","description":"Generates a countTable from a PEP for DESeq analysis","archived":false,"fork":false,"pushed_at":"2019-02-15T20:40:52.000Z","size":12786,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-05T04:44:27.946Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/databio.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-11-22T21:28:43.000Z","updated_at":"2020-03-04T14:19:57.000Z","dependencies_parsed_at":"2023-03-11T04:16:23.246Z","dependency_job_id":null,"html_url":"https://github.com/databio/DESeqPackager","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/databio/DESeqPackager","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FDESeqPackager","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FDESeqPackager/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FDESeqPackager/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FDESeqPackager/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/DESeqPackager/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FDESeqPackager/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266058481,"owners_count":23870157,"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":"2024-11-15T07:12:03.181Z","updated_at":"2025-07-20T02:36:47.681Z","avatar_url":"https://github.com/databio.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DESeqPackager\nFrom Aaron Gu\n\n```R\nDESeqPackager(pepr, data_source, gene_names, gene_counts)\n```\n\nDESeqPackager takes in an RNA-seq project in [PEP format](https://pepkit.github.io/docs/pepr/) and combines the data for each sample into a DESeq countDataSet structure. It's best used with output from the [rnapipe](https://github.com/databio/rnapipe) pipeline.\n\n### Required Packages\n\n- pepr\n- data.table\n\n## Quick Start\n\nThe quick start uses sample gene expression data available for download at `expr_tsv.tar.gz` from http://big.databio.org/example_data/deseq_packager/\n\nIn a new R file, load in the function\n```R\nsource(\"DESeqPackager.R\")\n```\n\nConstruct a pepr project using the yaml located in this repository\n```R\np = pepr::Project(file=\"project_config.yaml\")\n```\n\nRun DESeqPackager\n```R\ncountDataSet \u003c- DESeqPackager(p, \"data_source\", \"ensembl_gene_id\", \"FPKM\")\n```\n\n### Running DESeqPackager with BioConductor\n\n[BiocProject](http://code.databio.org/BiocProject/index.html) is another way to read in biological data in the PEP format. It can load both project metadata and sample data in a single line of code.\n\n```R\nbpArgs = BiocProject(file=\"project_config.yaml\", funcArgs=list(data_source=\"data_source\", gene_names=\"ensembl_gene_id\", gene_counts=\"FPKM\"))\ngetData(bpArgs)\n```\n\nAnother option is to put the `funcArgs` in the yaml file.\n```R\nbpArgs = BiocProject(file=\"project_config.yaml\")\ngetData(bpArgs)\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fdeseqpackager","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fdeseqpackager","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fdeseqpackager/lists"}