{"id":19624232,"url":"https://github.com/bioconductor/tenxbrainanalysis","last_synced_at":"2025-07-20T14:32:19.836Z","repository":{"id":78223535,"uuid":"113096325","full_name":"Bioconductor/TENxBrainAnalysis","owner":"Bioconductor","description":"R scripts for analyzing the 1.3 million brain cell data set from 10X Genomics","archived":false,"fork":false,"pushed_at":"2023-03-15T21:02:16.000Z","size":38,"stargazers_count":12,"open_issues_count":0,"forks_count":2,"subscribers_count":6,"default_branch":"devel","last_synced_at":"2025-04-28T05:35:05.461Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Bioconductor.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":"2017-12-04T21:19:32.000Z","updated_at":"2023-03-15T21:02:19.000Z","dependencies_parsed_at":"2024-11-11T11:39:09.606Z","dependency_job_id":null,"html_url":"https://github.com/Bioconductor/TENxBrainAnalysis","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Bioconductor/TENxBrainAnalysis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FTENxBrainAnalysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FTENxBrainAnalysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FTENxBrainAnalysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FTENxBrainAnalysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/TENxBrainAnalysis/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FTENxBrainAnalysis/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266139818,"owners_count":23882546,"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":"2024-11-11T11:37:21.780Z","updated_at":"2025-07-20T14:32:19.831Z","avatar_url":"https://github.com/Bioconductor.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Scripts for analyzing the 10X 1.3 million brain cell data\n\nThe scripts should be executed in the following order:\n\n- `intro.Rmd`: An introduction, duh.\n- `preprocess.Rmd`: Downloading the data and quality control\n- `cycle.Rmd`: Cell cycle phase assignment\n- `normalize.Rmd`: Calculation of cell-specific size factors\n- `variance.Rmd`: Identification of highly variable genes\n- `dimred.Rmd`: Dimensionality reduction with randomized PCA \n\nVarious output objects will be saved to `objects/`.\nA few of these objects are currently hosted at https://drive.google.com/open?id=1_0WbmJ2BriLKlyKEf1Bbb8K0_NwD9rw-.\nNote that `sce.rds` does not contain the actual counts or normalized expression values, and requires something like this:\n\n```r\nlibrary(TENxBrainData)\ntenx \u003c- TENxBrainData()\nsce \u003c- readRDS(\"sce.rds\")\ntenx \u003c- tenx[,colnames(sce)] # drop 19,672 cells from the raw TENxBrainData\ncounts(sce) \u003c- counts(tenx) # overwrite inbuilt absolute path\nlibrary(scater)\nsce \u003c- normalize(sce) # generate normalized expression values\n```\n\nThe `pics/make_pics.R` scripts will generate the figures used in the paper.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Ftenxbrainanalysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Ftenxbrainanalysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Ftenxbrainanalysis/lists"}