{"id":37677151,"url":"https://github.com/czbiohub-sf/protdata","last_synced_at":"2026-01-16T12:16:24.469Z","repository":{"id":310469692,"uuid":"980908295","full_name":"czbiohub-sf/protdata","owner":"czbiohub-sf","description":"Dataloader for common proteomics search engine outputs into AnnData format","archived":false,"fork":false,"pushed_at":"2025-11-20T00:33:50.000Z","size":989,"stargazers_count":9,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-11-20T02:26:12.446Z","etag":null,"topics":["anndata","proteomics","proteomics-datasets","python"],"latest_commit_sha":null,"homepage":"https://protdata.sf.czbiohub.org","language":"Python","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/czbiohub-sf.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-05-09T23:48:27.000Z","updated_at":"2025-11-20T00:34:22.000Z","dependencies_parsed_at":"2025-08-18T10:52:01.240Z","dependency_job_id":null,"html_url":"https://github.com/czbiohub-sf/protdata","commit_stats":null,"previous_names":["czbiohub-sf/protdata"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/czbiohub-sf/protdata","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/czbiohub-sf%2Fprotdata","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/czbiohub-sf%2Fprotdata/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/czbiohub-sf%2Fprotdata/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/czbiohub-sf%2Fprotdata/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/czbiohub-sf","download_url":"https://codeload.github.com/czbiohub-sf/protdata/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/czbiohub-sf%2Fprotdata/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478536,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T11:59:17.896Z","status":"ssl_error","status_checked_at":"2026-01-16T11:55:55.838Z","response_time":107,"last_error":"SSL_read: 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":["anndata","proteomics","proteomics-datasets","python"],"created_at":"2026-01-16T12:16:24.387Z","updated_at":"2026-01-16T12:16:24.457Z","avatar_url":"https://github.com/czbiohub-sf.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# protdata\n\n[![Test](https://github.com/czbiohub-sf/protdata/actions/workflows/test.yml/badge.svg)](https://github.com/czbiohub-sf/protdata/actions/workflows/test.yml)\n![PyPI - Version](https://img.shields.io/pypi/v/protdata)\n[![docs online](https://img.shields.io/badge/docs-online-blue)](https://protdata-czbiohub.vercel.app/)\n\n\u003ca href=\"https://protdata.sf.czbiohub.org\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/czbiohub-sf/protdata/refs/heads/main/docs/source/_static/img/protdata_schema.svg\"\n    class=\"dark-light\"\n    align=\"right\"\n    width=\"150\"\n    alt=\"image\"\n  /\u003e\n\u003c/a\u003e\n\nProteomics data loaders for the [AnnData](https://anndata.readthedocs.io/) format.\n\nThis package provides loader functions to import proteomics data (e.g., MaxQuant) into the AnnData structure for downstream analysis and easy integration with single-cell and multi-omics workflows.\n\n## Features\n\n- **Multiple formats**: Support for MaxQuant, FragPipe, DIA-NN, and mzTab files\n- **Reads metadata**: Automatically extracts and organizes sample and protein metadata\n\n## Installation\n\nProtdata has minimal dependencies listed in [pyproject.toml](https://github.com/czbiohub-sf/protdata/blob/main/pyproject.toml)\n\nTo install the latest release from PyPI, run:\n\n```bash\npip install protdata\n```\n\nOr install from source:\n```bash\ngit clone https://github.com/czbiohub-sf/protdata.git\ncd protdata\npip install -e . # or make setup-develop for developers\n```\n\n## Usage Example\n\n### MaxQuant Import\n\nYou can download an example proteinGroups [file here](https://github.com/czbiohub-sf/protdata/raw/main/data/proteinGroups.txt)\n```python\nimport protdata\n\nadata = load_maxquant_to_anndata(\"/path/to/proteinGroups.txt\")\nprint(adata)\n```\n\n### DIA-NN Import\n\nYou can download an example DIA-NN report [file here](https://github.com/czbiohub-sf/protdata/raw/main/data/report.pg_matrix.tsv)\n\n```python\nfrom protdata.io import read_diann\n\nadata = read_diann(\"/path/to/report.pg_matrix.tsv\")\nprint(adata)\n```\n\n### FragPipe Import\n\nYou can download an example FragPipe output [file here](https://github.com/czbiohub-sf/protdata/raw/main/data/combined_protein.tsv)\n\n```python\nfrom protdata.io import read_fragpipe\n\nadata = read_fragpipe(\"/path/to/combined_protein.tsv\")\nprint(adata)\n```\n\n### mzTab Import\n\nYou can download an example mzTab [file here](https://github.com/czbiohub-sf/protdata/raw/main/data/SILAC_SQ.mzTab)\n\n```python\nfrom protdata.io import read_mztab\n\nadata = read_mztab(\"/path/to/SILAC_SQ.mzTab\")\nprint(adata)\n```\n## Authors\n\n`protdata` is created and maintained by the [Computational Biology Platform](https://www.czbiohub.org/comp-biology/) at the [Chan Zuckerberg Biohub San Francisco](https://www.czbiohub.org/sf/).\n\nTo get in touch please use the [GihHub issues](https://github.com/czbiohub-sf/protdata/issues) page.\n\n## Contributing\n\nIf you want to contribute to `protdata`, please read the [Contribution Guide](https://protdata.sf.czbiohub.org/contributing.html)\n\n## Changelog\nSee [Release Notes](https://protdata.sf.czbiohub.org/release_notes.html)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fczbiohub-sf%2Fprotdata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fczbiohub-sf%2Fprotdata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fczbiohub-sf%2Fprotdata/lists"}