{"id":34701847,"url":"https://github.com/hubmapconsortium/py-hubmapbags","last_synced_at":"2026-05-26T03:35:48.072Z","repository":{"id":39989320,"uuid":"483779614","full_name":"hubmapconsortium/py-hubmapbags","owner":"hubmapconsortium","description":"Python package used to build the submission for the CFDE Search Portal","archived":false,"fork":false,"pushed_at":"2025-01-09T16:50:53.000Z","size":5194,"stargazers_count":1,"open_issues_count":18,"forks_count":2,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-01-09T17:52:02.429Z","etag":null,"topics":["data-wrangling"],"latest_commit_sha":null,"homepage":"","language":"Jupyter 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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["data-wrangling"],"created_at":"2025-12-24T22:53:08.545Z","updated_at":"2026-05-26T03:35:48.067Z","avatar_url":"https://github.com/hubmapconsortium.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# README\n\n## Examples\n\n### Get list of assay names\n\n```\nimport hubmapbags\nfrom datetime import datetime\nfrom pathlib import Path\n\nanswer = hubmapbags.apis.get_assay_types()\nprint(answer)\n```\n\nwill result in something like\n\n```\n['AF', 'ATACseq-bulk', 'cell-dive', 'CODEX', 'DART-FISH', 'IMC2D', 'IMC3D', 'lc-ms_label-free', 'lc-ms_labeled', 'lc-ms-ms_label-free', 'lc-ms-ms_labeled', 'LC-MS-untargeted', 'Lightsheet', 'MALDI-IMS', 'MIBI', 'NanoDESI', 'NanoPOTS', 'MxIF', 'PAS', 'bulk-RNA', 'SNARE-ATACseq2', 'SNARE-RNAseq2', 'scRNAseq-10xGenomics-v2', 'scRNAseq-10xGenomics-v3', 'sciATACseq', 'sciRNAseq', 'seqFish', 'seqFish_pyramid', 'snATACseq', 'snRNAseq-10xGenomics-v2', 'snRNAseq-10xGenomics-v3', 'Slide-seq', 'Targeted-Shotgun-LC-MS', 'TMT-LC-MS', 'WGS', 'LC-MS', 'MS', 'LC-MS_bottom_up', 'MS_bottom_up', 'LC-MS_top_down', 'MS_top_down']\n```\n\n### Get list of HuBMAP ids, UUIDs and status given an assay name\n\n```\nimport hubmapbags\nfrom datetime import datetime\nfrom pathlib import Path\n\nassay_name = 'AF'\nanswer = hubmapbags.apis.get_hubmap_ids( assay_name=assay_name )\nprint(answer)\n```\n\nwill result in something like\n\n```\n[{'uuid': '2f9e91ff774243ef11d148a2bf7a6822', 'hubmap_id': 'HBM268.FSPK.489', 'status': 'Published'}, {'uuid': 'dc289471333309925e46ceb9bafafaf4', 'hubmap_id': 'HBM279.SSXF.866', 'status': 'Published'}, {'uuid': '2bc6713576dda7c7e6378aec38df437d', 'hubmap_id': 'HBM447.NXPZ.263', 'status': 'Published'}, {'uuid': '57299edf509b218aa9b4c4a2e1d979bd', 'hubmap_id': 'HBM535.QCJS.935', 'status': 'Published'}, {'uuid': '02e13b9b3cdc939cca397c42c2981dd1', 'hubmap_id': 'HBM362.DLZS.564', 'status': 'Published'}, {'uuid': '46ed471a6b4ad5b97817ff2c26ef6ddd', 'hubmap_id': 'HBM873.FRQB.759', 'status': 'Published'}, {'uuid': '109162ed40ede274202eab96bf640fa4', 'hubmap_id': 'HBM739.JSGQ.673', 'status': 'Published'}, {'uuid': '5eb7d04d71566c53dfc9eb1c7346c68d', 'hubmap_id': 'HBM882.DMQM.597', 'status': 'Published'}, {'uuid': 'f54b458ca42f7112d0e0751c9ba41492', 'hubmap_id': 'HBM298.JRGF.528', 'status': 'Published'}, {'uuid': '6a037ddcb811f77f726b9f78e5d369a2', 'hubmap_id': 'HBM969.JXDC.887', 'status': 'Published'}]\n```\n\n---\nCopyright © 2020-2024 Pittsburgh Supercomputing Center. All Rights Reserved.\n\nThe [Biomedical Applications Group](https://www.psc.edu/biomedical-applications/) at the [Pittsburgh Supercomputing Center](http://www.psc.edu) in the [Mellon College of Science](https://www.cmu.edu/mcs/) at [Carnegie Mellon University](http://www.cmu.edu).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhubmapconsortium%2Fpy-hubmapbags","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhubmapconsortium%2Fpy-hubmapbags","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhubmapconsortium%2Fpy-hubmapbags/lists"}