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returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":[],"created_at":"2026-01-23T14:59:37.072Z","updated_at":"2026-01-23T14:59:37.821Z","avatar_url":"https://github.com/cellgeni.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# iRODS ranger\n\n## Install\n```bash\npip install git+https://github.com/cellgeni/iranger.git\n```\n\n## Usage\n\n### Load objects\n\n```python\nimport iranger\n\n# You can use your password directly\nir = iranger.setup(password='Your_iRODS_Password_Goes_Here')\n# ...or alternatively put your password in a file and use that instead\nir = iranger.setup(password_file='~/my_password_file')\n\n# load 10x cellranger output\nadata = ir.read(\"/seq/26280/cellranger/cellranger302_count_26280_FCAImmP7555847_GRCh38-1_2_0\")\n\n# load 10x spaceranger output\nadata = ir.read(\"/seq/illumina/spaceranger/spaceranger130_count__WSSKNKCLsp12887269_GRCh38-2020-A\")\n\n# load 10x spaceranger output with *raw counts*\nadata_raw = ir.read(\"/seq/illumina/spaceranger/spaceranger130_count__WSSKNKCLsp12887269_GRCh38-2020-A\", count_file=\"raw_feature_bc_matrix.h5\")\n\n# load 10x cellranger-arc output\nadata = ir.read(\"/seq/illumina/cellranger-arc/cellranger-arc101_count_1408ea687d742c7b571c62c7f441d372\")\n# if you only want gene experession\nadata_gex = adata[:, adata.var[\"feature_types\"]==\"Gene Expression\"]\n```\n\n#### Embeded iRODS metadata\n\nAnnData files will have an `_irods` key inside unstructured observations with the irods path and all the medata for the collection.\n\n```python\n\u003e\u003e\u003e adata.uns['_irods']\n{\n  'path': '/seq/26280/cellranger/cellranger302_count_26280_FCAImmP7555847_GRCh38-1_2_0',\n  'metadata': [{'name': 'library_type', 'value': 'Chromium single cell'}, {'name': 'study', 'value': 'FCA_ImmunoP'}, {'name': 'study_accession_number', 'value': 'EGAS00001002715'}, {'name': 'study_id', 'value': '5061'}, {'name': 'study_title', 'value': 'FCA_ImmunoP'}, {'name': 'id_run', 'value': '26280'}, {'name': 'sample', 'value': 'FCAImmP7555847'}, {'name': 'sample_id', 'value': '3775200'}, {'name': 'analysis_type', 'value': 'cellranger count'}, {'name': '10x:reference', 'value': '/nfs/srpipe_references/downloaded_from_10X/refdata-cellranger-GRCh38-1.2.0'}, {'name': '10x:pipeline', 'value': '/software/sciops/external/cellranger/3.0.2/cellranger'}, {'name': 'sample_lims', 'value': 'SQSCP'}, {'name': 'sample_uuid', 'value': '8b7789d6-7abf-11e8-8cef-68b599768938'}]\n}\n```\n\n#### iRODS environment file\n\nThe package requires an `irods_environment.json` file present in the machine. The standard location is:\n```bash\n~/.irods/irods_environment.json\n```\n\nShould you whish to have it in a different location you'll have to be explicit about it, for example:\n\n```python\nir = iranger.setup(\n    irods_environment='/path/to/my/irods_environment.json',\n    password_file='/safe/path/to/my_password_file'\n)\n```\n\n### Search objects\n\n```python\nimport iranger\n\nir = iranger.setup(password_file='~/my_password_file')\n\nresults = ir.find(sample='WSSKNKCLsp12887269')\n\nfor result in results:\n    print(result['path'])\n    for meta in result['metadata']:\n        print(meta)\n\n...\n\n'/seq/illumina/spaceranger/spaceranger130_count__WSSKNKCLsp12887269_GRCh38-2020-A'\n\n{'sample_common_name': 'human'}\n{'library_type': 'Chromium Visium'}\n{'study': 'HCA Skin Adult WSSS Spatial_KCL'}\n{'study_accession_number': 'EGAS00001005404'}\n{'study_id': '6551'}\n{'study_title': 'HCA Skin Adult WSSS Spatial_KCL'}\n{'id_run': '44928'}\n{'sample': 'WSSKNKCLsp12887269'}\n{'sample_accession_number': 'EGAN00003542204'}\n{'sample_id': '8276456'}\n{'id_run': '44929'}\n{'10x:reference': '/nfs/srpipe_references/downloaded_from_10X/refdata-gex-GRCh38-2020-A'}\n{'analysis_type': 'spaceranger count'}\n{'10x:pipeline': '/software/sciops/external/spaceranger/1.3.0/spaceranger'}\n{'sample_lims': 'SQSCP'}\n{'sample_uuid': '7c579590-d060-11ec-a674-fa163eac3af7'}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcellgeni%2Firanger","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcellgeni%2Firanger","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcellgeni%2Firanger/lists"}