https://github.com/czbiohub-sf/protdata
Dataloader for common proteomics search engine outputs into AnnData format
Science Score: 26.0%
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○Scientific vocabulary similarity
Low similarity (17.3%) to scientific vocabulary
Keywords
Repository
Dataloader for common proteomics search engine outputs into AnnData format
Basic Info
- Host: GitHub
- Owner: czbiohub-sf
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://protdata.sf.czbiohub.org
- Size: 818 KB
Statistics
- Stars: 5
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 1
Topics
Metadata Files
README.md
protdata
Proteomics data loaders for the AnnData format.
This 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.
Features
- Multiple formats: Support for MaxQuant, FragPipe, DIA-NN, and mzTab files
- Reads metadata: Automatically extracts and organizes sample and protein metadata
Installation
Protdata has minimal dependencies listed in pyproject.toml
To install the latest release from PyPI, run:
bash
pip install protdata
Or install from source:
bash
git clone https://github.com/czbiohub-sf/protdata.git
cd protdata
pip install -e . # or make setup-develop for developers
Usage Example
MaxQuant Import
You can download an example proteinGroups file here ```python import protdata
adata = loadmaxquantto_anndata("/path/to/proteinGroups.txt") print(adata) ```
DIA-NN Import
You can download an example DIA-NN report file here
```python from protdata.io import read_diann
adata = readdiann("/path/to/report.pgmatrix.tsv") print(adata) ```
FragPipe Import
You can download an example FragPipe output file here
```python from protdata.io import read_fragpipe
adata = readfragpipe("/path/to/combinedprotein.tsv") print(adata) ```
mzTab Import
You can download an example mzTab file here
```python from protdata.io import read_mztab
adata = readmztab("/path/to/SILACSQ.mzTab") print(adata) ```
Authors
protdata is created and maintained by the Computational Biology Platform at the Chan Zuckerberg Biohub San Francisco.
To get in touch please use the GihHub issues page.
Contributing
If you want to contribute to protdata, please read the Contribution Guide
Changelog
See Release Notes
Owner
- Name: Chan Zuckerberg Biohub San Francisco
- Login: czbiohub-sf
- Kind: organization
- Location: San Francisco
- Website: https://www.czbiohub.org/sf/
- Repositories: 1
- Profile: https://github.com/czbiohub-sf
GitHub Events
Total
- Watch event: 6
- Issue comment event: 1
- Push event: 1
- Pull request event: 1
- Create event: 1
Last Year
- Watch event: 6
- Issue comment event: 1
- Push event: 1
- Pull request event: 1
- Create event: 1
Packages
- Total packages: 1
-
Total downloads:
- pypi 203 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
pypi.org: protdata
Proteomics data loaders for AnnData format.
- Documentation: https://protdata.readthedocs.io/
- License: bsd-3-clause
-
Latest release: 0.1.4
published 7 months ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v4 composite
- actions/download-artifact v4 composite
- actions/setup-python v5 composite
- actions/upload-artifact v4 composite
- pypa/gh-action-pypi-publish release/v1 composite
- actions/checkout v4 composite
- actions/setup-python v5 composite
- anndata *
- numpy *
- pandas *
- pyteomics *