protdata

protdata#

Test PyPI - Version docs online

image

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:

pip install protdata

Or install from source:

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

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

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

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

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 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

Indices and tables#

Contents