https://github.com/czbiohub-sf/protdata
Dataloader for common proteomics search engine outputs into AnnData format
https://github.com/czbiohub-sf/protdata
anndata proteomics proteomics-datasets python
Last synced: 6 months ago
JSON representation
Dataloader for common proteomics search engine outputs into AnnData format
- Host: GitHub
- URL: https://github.com/czbiohub-sf/protdata
- Owner: czbiohub-sf
- License: bsd-3-clause
- Created: 2025-05-09T23:48:27.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-11-20T00:33:50.000Z (8 months ago)
- Last Synced: 2025-11-20T02:26:12.446Z (8 months ago)
- Topics: anndata, proteomics, proteomics-datasets, python
- Language: Python
- Homepage: https://protdata.sf.czbiohub.org
- Size: 966 KB
- Stars: 9
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# protdata
[](https://github.com/czbiohub-sf/protdata/actions/workflows/test.yml)
[](https://protdata-czbiohub.vercel.app/)
Proteomics data loaders for the [AnnData](https://anndata.readthedocs.io/) 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](https://github.com/czbiohub-sf/protdata/blob/main/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](https://github.com/czbiohub-sf/protdata/raw/main/data/proteinGroups.txt)
```python
import protdata
adata = load_maxquant_to_anndata("/path/to/proteinGroups.txt")
print(adata)
```
### DIA-NN Import
You can download an example DIA-NN report [file here](https://github.com/czbiohub-sf/protdata/raw/main/data/report.pg_matrix.tsv)
```python
from protdata.io import read_diann
adata = read_diann("/path/to/report.pg_matrix.tsv")
print(adata)
```
### FragPipe Import
You can download an example FragPipe output [file here](https://github.com/czbiohub-sf/protdata/raw/main/data/combined_protein.tsv)
```python
from protdata.io import read_fragpipe
adata = read_fragpipe("/path/to/combined_protein.tsv")
print(adata)
```
### mzTab Import
You can download an example mzTab [file here](https://github.com/czbiohub-sf/protdata/raw/main/data/SILAC_SQ.mzTab)
```python
from protdata.io import read_mztab
adata = read_mztab("/path/to/SILAC_SQ.mzTab")
print(adata)
```
## Authors
`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/).
To get in touch please use the [GihHub issues](https://github.com/czbiohub-sf/protdata/issues) page.
## Contributing
If you want to contribute to `protdata`, please read the [Contribution Guide](https://protdata.sf.czbiohub.org/contributing.html)
## Changelog
See [Release Notes](https://protdata.sf.czbiohub.org/release_notes.html)