{"id":13774404,"url":"https://github.com/cellgeni/sceasy","last_synced_at":"2026-01-23T14:59:26.122Z","repository":{"id":43332137,"uuid":"197408578","full_name":"cellgeni/sceasy","owner":"cellgeni","description":"A package to help convert different single-cell data formats to each other","archived":false,"fork":false,"pushed_at":"2024-02-28T10:07:24.000Z","size":76,"stargazers_count":328,"open_issues_count":45,"forks_count":51,"subscribers_count":8,"default_branch":"master","last_synced_at":"2024-04-18T05:37:17.310Z","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/cellgeni.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":"2019-07-17T14:46:01.000Z","updated_at":"2024-08-03T17:08:44.930Z","dependencies_parsed_at":"2024-08-03T17:18:47.006Z","dependency_job_id":null,"html_url":"https://github.com/cellgeni/sceasy","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2Fsceasy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2Fsceasy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2Fsceasy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2Fsceasy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cellgeni","download_url":"https://codeload.github.com/cellgeni/sceasy/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225022146,"owners_count":17408566,"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":"2024-08-03T17:01:26.390Z","updated_at":"2026-01-23T14:59:26.053Z","avatar_url":"https://github.com/cellgeni.png","language":"R","readme":"# sceasy\n\n`sceasy` is a package that helps easy conversion of different single-cell data formats to each other. Converting to AnnData creates a file that can be directly used in [cellxgene](https://github.com/chanzuckerberg/cellxgene) which is an interactive explorer for single-cell transcriptomics datasets.\n\n\n| 💡 for h5da to rds conversion also see [https://github.com/cellgeni/schard](https://github.com/cellgeni/schard) |\n| ----------------------------------------------------------------------------------------------- |\n\n\n\u003e ### Warning\n\u003e Before installing the conda packages below please first create a new conda environment EnvironmentName and activate it. Everything else can be installed in R.\n\n\n## Installation\n\nsceasy is installable either as a bioconda package:\n\n```conda install -c bioconda r-sceasy```\n\nor as an R package:\n\n```devtools::install_github(\"cellgeni/sceasy\")```\n\nwhich will require the biconductor packages BiocManager and LoomExperiment:\n\n```\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(c(\"LoomExperiment\", \"SingleCellExperiment\"))\n```\n\nTo use sceasy ensure the anndata package is installed:\n\n```conda install anndata -c bioconda```\n\nOptionally, if you plan to convert between loom and anndata, please also ensure that the `loompy` package is installed:\n\n```conda install loompy  -c bioconda```\n\nYou will also need to install reticulate package:\n\n```install.packages('reticulate')```\n\n\n## Usage\n\nBefore converting your data please load the following libraries in your R session:\n\n```\nlibrary(sceasy)\nlibrary(reticulate)\nuse_condaenv('EnvironmentName')\nloompy \u003c- reticulate::import('loompy')\n```\n\n**Seurat to AnnData**\n\n```\nsceasy::convertFormat(seurat_object, from=\"seurat\", to=\"anndata\",\n                       outFile='filename.h5ad')\n```\n\n**AnnData to Seurat**\n\n```\nsceasy::convertFormat(h5ad_file, from=\"anndata\", to=\"seurat\",\n                       outFile='filename.rds')\n```\n                       \n**Seurat to SingleCellExperiment**\n\n```\nsceasy::convertFormat(seurat_object, from=\"seurat\", to=\"sce\",\n                       outFile='filename.rds')\n```\n   \n**SingleCellExperiment to AnnData**\n\n```\nsceasy::convertFormat(sce_object, from=\"sce\", to=\"anndata\",\n                       outFile='filename.h5ad')\n```\n                       \n**SingleCellExperiment to Loom**\n\n```\nsceasy::convertFormat(sce_object, from=\"sce\", to=\"loom\",\n                       outFile='filename.loom')\n```\n                       \n**Loom to AnnData**\n\n```\nsceasy::convertFormat('filename.loom', from=\"loom\", to=\"anndata\",\n                       outFile='filename.h5ad')\n```\n                       \n**Loom to SingleCellExperiment**\n\n```\nsceasy::convertFormat('filename.loom', from=\"loom\", to=\"sce\",\n                       outFile='filename.rds')\n```\n","funding_links":[],"categories":["Single Cell"],"sub_categories":["scRNA Analysis Pipelines"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcellgeni%2Fsceasy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcellgeni%2Fsceasy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcellgeni%2Fsceasy/lists"}