{"id":24529095,"url":"https://github.com/saezlab/process_rnaseq_cellines","last_synced_at":"2026-07-03T13:07:04.883Z","repository":{"id":68993155,"uuid":"199878612","full_name":"saezlab/process_rnaseq_cellines","owner":"saezlab","description":"Processing RNAseq data from Cell Lines. From raw data to normalised, voom and ComBat batch-correction","archived":false,"fork":false,"pushed_at":"2020-11-11T12:38:10.000Z","size":2577,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-22T07:37:40.549Z","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":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/saezlab.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":"2019-07-31T15:04:15.000Z","updated_at":"2022-06-17T14:39:12.000Z","dependencies_parsed_at":null,"dependency_job_id":"3d943b1f-627c-4eff-8fa7-19470bc0f095","html_url":"https://github.com/saezlab/process_rnaseq_cellines","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/saezlab%2Fprocess_rnaseq_cellines","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fprocess_rnaseq_cellines/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fprocess_rnaseq_cellines/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fprocess_rnaseq_cellines/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/process_rnaseq_cellines/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243769949,"owners_count":20345215,"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":"2025-01-22T07:34:46.784Z","updated_at":"2026-07-03T13:06:59.850Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# process_rnaseq_cellines\nProcessing RNAseq data from Cell Lines. The process_rnaseq_cellines_* files\nare pipelines that follow the next steps:\n\n - Imputes 0 to NA values\n - Removes samples exeding genes with 0\n - Removes non-expressed genes with average CPM \u003c=0\n - Normalises through TMM method\n - Runs Voom transformation\n - Uses ComBat for Batch correction of voom transformed data \n - Merges duplicates by the mean\n\nIn the wiki of this repo the exploratory analysis of the data can be found.\n\n# Technical details\n\nR version 3.6.0 (2019-04-26)\nPlatform: x86_64-apple-darwin15.6.0 (64-bit)\nRunning under: macOS Mojave 10.14.5\n\nPackages:\n\n- data.table 1.12.2\n- dplyr 0.8.1\n- stringr 1.4.0\n- limma 3.40.2\n- sva 3.32.1\n- edgeR 3.26.4\n- ggplot2 3.1.1\n- ggforce 0.2.2\n- ggfortify 0.4.7\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fprocess_rnaseq_cellines","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fprocess_rnaseq_cellines","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fprocess_rnaseq_cellines/lists"}