{"id":16320097,"url":"https://github.com/helenalc/bc2_2019-workshop_multi-scrna-seq","last_synced_at":"2026-02-10T11:37:32.556Z","repository":{"id":82290201,"uuid":"205326453","full_name":"HelenaLC/BC2_2019-workshop_multi-scRNA-seq","owner":"HelenaLC","description":null,"archived":false,"fork":false,"pushed_at":"2019-09-09T06:59:53.000Z","size":3271,"stargazers_count":1,"open_issues_count":1,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-08-12T09:31:38.065Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","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/HelenaLC.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":"2019-08-30T07:14:10.000Z","updated_at":"2019-09-09T06:59:55.000Z","dependencies_parsed_at":null,"dependency_job_id":"cc92139f-ced9-46e5-bafa-5e4a6b6d54ab","html_url":"https://github.com/HelenaLC/BC2_2019-workshop_multi-scRNA-seq","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/HelenaLC/BC2_2019-workshop_multi-scRNA-seq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FBC2_2019-workshop_multi-scRNA-seq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FBC2_2019-workshop_multi-scRNA-seq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FBC2_2019-workshop_multi-scRNA-seq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FBC2_2019-workshop_multi-scRNA-seq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/HelenaLC","download_url":"https://codeload.github.com/HelenaLC/BC2_2019-workshop_multi-scRNA-seq/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FBC2_2019-workshop_multi-scRNA-seq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29298507,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-10T10:40:02.018Z","status":"ssl_error","status_checked_at":"2026-02-10T10:38:28.459Z","response_time":65,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2024-10-10T22:29:04.712Z","updated_at":"2026-02-10T11:37:32.540Z","avatar_url":"https://github.com/HelenaLC.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BC2_2019-workshop_multi-scRNA-seq\n\n### Software installation\n\nFor this tutorial, you will need R 3.6, which you can download from [https://stat.ethz.ch/CRAN/](https://stat.ethz.ch/CRAN/).\n\nWe will, however, need to access the *devel* versions of various Bioconductor packages and with R 3.6, you can follow the code below (submitted to the terminal) to get a set of packages that should be compatible.  First, tell the `BiocManager` package that *devel* should be used:\n\n```\nif (!requireNamespace(\"BiocManager\", quietly=TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(version = \"devel\") # will get prompted\n```\n\nFor the steps below, you should be able to cut-and-paste the commands into an active session (and wait for packages and dependencies to be installed):\n```\nBiocManager::install(\"remotes\")\n\nSys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS=\"true\")\nBiocManager::install(\"HelenaLC/muscat\")\n\npkgs \u003c- c(\"M3C\",\"Seurat\",\"UpSetR\",\"cowplot\",\n          \"msigdbr\",\"org.Mm.eg.db\",\"pheatmap\",\n          \"scds\",\"scran\",\"topGO\",\"ExperimentHub\")\nBiocManager::install(pkgs)\n\nBiocManager::install(\"plger/scDblFinder\")\n```\n\n### Data downloads\n\nFor the pratical part of the workshop, we will be analyzing a replicated two-condition dataset of brain cortex tissue from mice treated with lipopolysaccharide (LPS), which is available [HERE](http://imlspenticton.uzh.ch/teaching/BC2_2019-workshop_multi-scRNA-seq).\n\n* **1-SCE_reduced.rds**: `SingleCellExperiment` (SCE) subset of the LPS dataset from Crowell *et al.*\u003csup\u003e[1](#f1)\u003c/sup\u003e\n* **2-SO_integrated.rds**: `SeuratObject` obtained after preprocessing \u0026 integration\n* **3-SCE_clustered.rds**: final clustered \u0026 annotated SCE for downstream analyses\n\n\u003ca name=\"f1\"\u003e[1]\u003c/a\u003e: \nCrowell HL, Soneson C\\*, Germain P-L\\*,  \nCalini D, Collin L, Raposo C, Malhotra D \u0026 Robinson MD:  \nOn the discovery of population-specific state transitions from  \nmulti-sample multi-condition single-cell RNA sequencing data.  \n*bioRxiv* **713412** (July, 2019). doi: [10.1101/713412](https://doi.org/10.1101/713412)","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhelenalc%2Fbc2_2019-workshop_multi-scrna-seq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhelenalc%2Fbc2_2019-workshop_multi-scrna-seq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhelenalc%2Fbc2_2019-workshop_multi-scrna-seq/lists"}