{"id":23957309,"url":"https://github.com/fperraudeau/singlecellworkflow","last_synced_at":"2025-09-12T15:32:08.021Z","repository":{"id":71020785,"uuid":"90190906","full_name":"fperraudeau/singlecellworkflow","owner":"fperraudeau","description":"Tutorial for the analysis of scRNA-seq data in R","archived":false,"fork":false,"pushed_at":"2018-08-28T21:51:43.000Z","size":155547,"stargazers_count":17,"open_issues_count":1,"forks_count":6,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-01-06T16:54:19.506Z","etag":null,"topics":["bioconductor","clustering","differential-expression","dimensionality-reduction","lineage","normalization","r","single-cell","single-cell-rna-seq","workflow"],"latest_commit_sha":null,"homepage":"","language":"TeX","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/fperraudeau.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-05-03T20:32:31.000Z","updated_at":"2024-10-26T11:27:11.000Z","dependencies_parsed_at":"2023-04-12T16:47:53.450Z","dependency_job_id":null,"html_url":"https://github.com/fperraudeau/singlecellworkflow","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/fperraudeau/singlecellworkflow","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fperraudeau%2Fsinglecellworkflow","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fperraudeau%2Fsinglecellworkflow/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fperraudeau%2Fsinglecellworkflow/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fperraudeau%2Fsinglecellworkflow/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fperraudeau","download_url":"https://codeload.github.com/fperraudeau/singlecellworkflow/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fperraudeau%2Fsinglecellworkflow/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274831537,"owners_count":25357882,"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":"2025-09-12T02:00:09.324Z","response_time":60,"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":["bioconductor","clustering","differential-expression","dimensionality-reduction","lineage","normalization","r","single-cell","single-cell-rna-seq","workflow"],"created_at":"2025-01-06T16:54:06.702Z","updated_at":"2025-09-12T15:32:08.010Z","avatar_url":"https://github.com/fperraudeau.png","language":"TeX","readme":"# Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference\n\n[![DOI](https://zenodo.org/badge/90190906.svg)](https://zenodo.org/badge/latestdoi/90190906)\n\nThis repository is designed to provide a tutorial for the analysis of scRNA-seq data in R. It covers four main steps: (1) dimensionality reduction accounting for zero inflation and over-dispersion and adjusting for gene and cell-level covariates; (2) robust and stable cell clustering using resampling-based sequential ensemble clustering; (3) inference of cell lineages and ordering of the cells by developmental progression along lineages; and (4) DE analysis along lineages. The workflow is general and flexible, allowing the user to sustitute the statistical method used in each step by a different method. We hope our proposed workflow will ease technical aspects of scRNA-seq data analysis and help with the discovery of novel biological insights.\n\n\n## Dependencies\n\nTo be able to run [workflow.Rmd](https://github.com/fperraudeau/singlecellworkflow/blob/master/workflow/workflow.Rmd), you need\n\n### Bioconductor\n\n- BiocParallel\n- clusterExperiment\n- scone\n- zinbwave\n\n### GitHub\n- slingshot (https://github.com/kstreet13/slingshot)\n\n### CRAN\n- doParallel\n- gam\n- RColorBrewer\n\n\nNote that you need the devel versions\nof the Bioconductor packages `scone (\u003e=1.1.2)`, `zinbwave (\u003e=0.99.6)`, and `clusterExperiment (\u003e=1.3.2)`. We recommend running Bioconductor 3.6 (currently the devel version; see https://www.bioconductor.org/developers/how-to/useDevel/).\n\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffperraudeau%2Fsinglecellworkflow","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffperraudeau%2Fsinglecellworkflow","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffperraudeau%2Fsinglecellworkflow/lists"}