{"id":22795126,"url":"https://github.com/dmalzl/yorisc","last_synced_at":"2025-08-07T01:33:41.946Z","repository":{"id":139731139,"uuid":"383515754","full_name":"dmalzl/yoRISC","owner":"dmalzl","description":"A bit of code to interconvert objects between the Seurat and RISC environments for scRNA-seq data analysis","archived":false,"fork":false,"pushed_at":"2021-07-08T14:18:04.000Z","size":14,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-30T17:46:34.416Z","etag":null,"topics":["bioinformatics","scrna-seq-analysis","seurat-objects"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dmalzl.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":"2021-07-06T15:27:57.000Z","updated_at":"2021-07-08T14:18:07.000Z","dependencies_parsed_at":"2023-05-06T15:31:57.328Z","dependency_job_id":null,"html_url":"https://github.com/dmalzl/yoRISC","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/dmalzl/yoRISC","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmalzl%2FyoRISC","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmalzl%2FyoRISC/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmalzl%2FyoRISC/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmalzl%2FyoRISC/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dmalzl","download_url":"https://codeload.github.com/dmalzl/yoRISC/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmalzl%2FyoRISC/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":269185585,"owners_count":24374620,"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":"2025-08-06T02:00:09.910Z","response_time":99,"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":["bioinformatics","scrna-seq-analysis","seurat-objects"],"created_at":"2024-12-12T04:13:33.742Z","updated_at":"2025-08-07T01:33:41.897Z","avatar_url":"https://github.com/dmalzl.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# yoRISC\nA bit of code to interconvert objects between the Seurat and RISC environments for scRNA-seq data analysis.\nThis source was mainly compiled by following the [RISC guide](https://github.com/bioinfoDZ/RISC/blob/master/Seurat_to_RISC.pdf) to convert Seurat object to RISC object and getting insight from looking at the source code of the [Seurat package](https://github.com/satijalab/seurat) (mainly on how their IntegrateData and RunPCA methods would work). The code was tested with the main functionality of Seurat for a generic scRNA-seq analysis. To run the conversion functions as presented in the `conversion.R` script you need the following packages\n\n- [RISC 1.0.0](https://github.com/bioinfoDZ/RISC)\n- [SeuratDisk 0.0.0.9019](https://github.com/mojaveazure/seurat-disk)    \n- [SeuratObject 4.0.0](https://github.com/mojaveazure/seurat-object)\n- [Seurat 4.0.1](https://satijalab.org/seurat/articles/install.html)\n\nFor any additonal code presented in the `risc_integration.Rmd` you also have to install\n- [gridExtra 2.3](https://cran.r-project.org/web/packages/gridExtra/index.html)\n- [ggplot2 3.3.3](https://ggplot2.tidyverse.org/)\n- [dplyr 1.0.5](https://dplyr.tidyverse.org/)\n- [tidyverse 1.3.1](https://www.tidyverse.org/)\n- [BiocManager 1.30.12](https://www.bioconductor.org/install/)\n- [celldex 1.0.0](https://bioconductor.org/packages/release/data/experiment/html/celldex.html)\n- [pheatmap 1.0.12](https://cran.r-project.org/web/packages/pheatmap/index.html)\n- [SingleR 1.4.1](https://www.bioconductor.org/packages/release/bioc/html/SingleR.html)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdmalzl%2Fyorisc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdmalzl%2Fyorisc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdmalzl%2Fyorisc/lists"}