{"id":13958697,"url":"https://github.com/theislab/scarches","last_synced_at":"2025-10-11T02:57:43.850Z","repository":{"id":40269863,"uuid":"201998885","full_name":"theislab/scarches","owner":"theislab","description":"Reference mapping for single-cell genomics","archived":false,"fork":false,"pushed_at":"2025-05-22T12:21:13.000Z","size":864922,"stargazers_count":365,"open_issues_count":59,"forks_count":59,"subscribers_count":11,"default_branch":"master","last_synced_at":"2025-05-22T14:06:36.537Z","etag":null,"topics":["batch-correction","data-integration","deep-learning","human-cell-atlas","multimodal-deep-learning","multiomics","rna-seq-analysis","scrna-seq","single-cell","single-cell-genomics"],"latest_commit_sha":null,"homepage":"https://docs.scarches.org/en/latest/","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/theislab.png","metadata":{"files":{"readme":"README.rst","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,"zenodo":null}},"created_at":"2019-08-12T19:51:11.000Z","updated_at":"2025-05-22T12:21:18.000Z","dependencies_parsed_at":"2024-01-03T06:30:54.750Z","dependency_job_id":"6992f2f8-5136-4ae3-8823-5cb9b9cc1ea7","html_url":"https://github.com/theislab/scarches","commit_stats":{"total_commits":1076,"total_committers":37,"mean_commits":29.08108108108108,"dds":0.6561338289962826,"last_synced_commit":"598358d74b83846fe034e4165058ac605f0dbc2d"},"previous_names":[],"tags_count":16,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/scarches","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fscarches","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fscarches/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fscarches/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fscarches/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/scarches/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fscarches/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266221280,"owners_count":23894966,"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":["batch-correction","data-integration","deep-learning","human-cell-atlas","multimodal-deep-learning","multiomics","rna-seq-analysis","scrna-seq","single-cell","single-cell-genomics"],"created_at":"2024-08-08T13:01:48.660Z","updated_at":"2025-10-11T02:57:38.813Z","avatar_url":"https://github.com/theislab.png","language":"Jupyter Notebook","funding_links":[],"categories":["其他_生物医药","Machine Learning Tasks and Models"],"sub_categories":["网络服务_其他","Foundation Models"],"readme":".. raw:: html\n\n \u003cimg src=\"https://user-images.githubusercontent.com/33202701/187203672-e0415eec-1278-4b2a-a097-5bb8b6ab694f.svg\" width=\"300px\" height=\"200px\" align=\"center\"\u003e\n\n|PyPI| |PyPIDownloads| |Docs|\n\n\nSingle-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data.\n\n\nWhat is scArches?\n-------------------------------\nscArches allows your single-cell query data to be analyzed by integrating it into a reference atlas. By mapping your data into an integrated reference you can transfer cell-type annotation from reference to query, identify disease states by mapping to healthy atlas, and advanced applications such as imputing missing data modalities or spatial locations.\n\n\nUsage and installation\n-------------------------------\nSee `here \u003chttps://scarches.readthedocs.io/\u003e`_ for documentation and tutorials.\n\nSupport and contribute\n-------------------------------\nIf you have a question or new architecture or a model that could be integrated into our pipeline, you can\npost an `issue \u003chttps://github.com/theislab/scarches/issues/new\u003e`__ or reach us by `email \u003cmo.lotfollahi@gmail.com\u003e`_.\n\nReference\n-------------------------------\nIf scArches is helpful in your research, please consider citing the following `paper \u003chttps://www.nature.com/articles/s41587-021-01001-7\u003e`_:\n::\n\n\n       @article{lotfollahi2021mapping,\n         title={Mapping single-cell data to reference atlases by transfer learning},\n         author={Lotfollahi, Mohammad and Naghipourfar, Mohsen and Luecken, Malte D and Khajavi,\n         Matin and B{\\\"u}ttner, Maren and Wagenstetter, Marco and Avsec, {\\v{Z}}iga and Gayoso,\n         Adam and Yosef, Nir and Interlandi, Marta and others},\n         journal={Nature Biotechnology},\n         pages={1--10},\n         year={2021},\n         publisher={Nature Publishing Group}}\n\n\n\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/scarches.svg\n   :target: https://pypi.org/project/scarches\n\n.. |PyPIDownloads| image:: https://pepy.tech/badge/scarches\n   :target: https://pepy.tech/project/scarches\n\n.. |Docs| image:: https://readthedocs.org/projects/scarches/badge/?version=latest\n   :target: https://scarches.readthedocs.io\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fscarches","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fscarches","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fscarches/lists"}