{"id":22631875,"url":"https://github.com/alleninstitute/cell_type_mapper","last_synced_at":"2025-04-11T20:10:33.308Z","repository":{"id":180249307,"uuid":"595817000","full_name":"AllenInstitute/cell_type_mapper","owner":"AllenInstitute","description":"Repository for storing prototype functionality implementations for the BKP","archived":false,"fork":false,"pushed_at":"2025-04-02T23:40:57.000Z","size":37764,"stargazers_count":24,"open_issues_count":5,"forks_count":5,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-04-03T00:26:39.581Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/AllenInstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.txt","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":"2023-01-31T21:40:41.000Z","updated_at":"2025-03-19T17:54:18.000Z","dependencies_parsed_at":"2024-03-14T18:49:49.696Z","dependency_job_id":"c7098202-51a3-4316-84a1-b144a840139f","html_url":"https://github.com/AllenInstitute/cell_type_mapper","commit_stats":null,"previous_names":["alleninstitute/cell_type_mapper"],"tags_count":32,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fcell_type_mapper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fcell_type_mapper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fcell_type_mapper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fcell_type_mapper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenInstitute","download_url":"https://codeload.github.com/AllenInstitute/cell_type_mapper/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248473127,"owners_count":21109628,"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":"2024-12-09T02:13:51.493Z","updated_at":"2025-04-11T20:10:33.298Z","avatar_url":"https://github.com/AllenInstitute.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Cell Type Mapper\n\n## Overview\n\nThis code provides a python package for mapping single sell RNA sequencing data\nonto a cell type taxonomy such as that provided by the Allen Institute for Brain\nScience.\n\n## Installation\n\nTo install this library, clone the repository, then (ideally from a clean\npython environment)\n\n- Run `pip install -e .` from the root directory of this repository to install\nthis package itself.\n\nThis package has been tested extensively with python 3.9. We have no reason to\nbelieve that it will not also run with python 3.8 and 3.10.\n\n## Common use cases\n\nIn addition to the documentation referenced below, we provide several\nJupyter notebooks detailing common use cases for this code.\n\n### Submitting data to online MapMyCells tool\n\nThe code in this repository provides the backend for the Allen Institute's\nonline [MapMyCells](https://knowledge.brain-map.org/mapmycells/process/) tool.\n[This notebook](https://github.com/AllenInstitute/cell_type_mapper/blob/update/docs/250304/examples/explore_mapping_results.ipynb)\nwalks the user through the process of downloading actual data, formatting\nit to be submitted to MapMyCells, and then downloading and interpreting the\nresults. You may also want to consult [this page](https://github.com/AllenInstitute/cell_type_mapper/blob/update/docs/250304/docs/output.md)\nfor detailed documentation of the output produced by the mapping code.\n\n### Mapping to Allen Institute taxonomies on your own machine\n\nIf you want to run the code on your own machine, but still want to map\nto the taxonomies supported by the on-line MapMyCells tool, consult\n[this page](https://github.com/AllenInstitute/cell_type_mapper/blob/update/docs/250304/docs/input_data_files/running_online_taxonomies_locally.md) and Section 8\nof [this Jupyter notebook.](https://github.com/AllenInstitute/cell_type_mapper/blob/update/docs/250304/examples/mapping_to_subset_of_abc_atlas_data.ipynb)\n\n### Mapping to a user-defined taxonomy\n\n[This Jupyter notebook](https://github.com/AllenInstitute/cell_type_mapper/blob/update/docs/250304/examples/full_mapping_pipeline.ipynb)\nwalks the user through the process of creating a new taxonomy from cartoon\ndata (generated by the notebook) and mapping unlabeled data to that\ntaxonomy.\n\n### Creating and mapping to a taxonomy defined from a subset of the Allen Institute's data\n\n[This Jupyter notebook](https://github.com/AllenInstitute/cell_type_mapper/blob/update/docs/250304/examples/mapping_to_subset_of_abc_atlas_data.ipynb)\nwalks the user through the process of downloading a subset of the\nAllen Institute's Whole Mouse Brain data using the\n[abc_atlas_access tool](https://alleninstitute.github.io/abc_atlas_access/intro.html),\ncreating a taxonomy based solely on that subset of the data,\nand mapping data to that new taxonomy.\n\n## Detailed documentation\n\nThe recommended workflow for running this code is\n[here.](docs/mapping_cells.md)\n\nDocumentation of the output produced by this code can be found\n[here.](docs/output.md)\n\n## Level of support\n\nWe are providing this tool to the community and any and all who want to use it.\nIssues and pull requests are welcome, however, this code is also intended\nas part of the backend for the Allen Institute Brain Knowledge Platform. As\nsuch, issues and pull requests may be declined if they interfere with\nthe functionality required to support that service.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falleninstitute%2Fcell_type_mapper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falleninstitute%2Fcell_type_mapper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falleninstitute%2Fcell_type_mapper/lists"}