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Proteomics Python Packages

Python packages with the GitHub topic proteomics. Sorted by relevance, with stars and monthly downloads.
OpenMS
pyopenms

The codebase of the OpenMS project

182K 593 429
pachterlab
gget

🧬 gget enables efficient querying of genomic reference databases

37K 1K 85
MannLabs
alphabase

Infrastructure of AlphaX ecosystem

8K 54 13
compomics
ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.

7K 49 19
microbiomedata
nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

7K 46 10
snijderlab
rustyms

A library to handle proteomic mass spectrometry data and match peptides to spectra.

5K 47 10
wfondrie
depthcharge-ms

A deep learning toolkit for mass spectrometry

5K 90 26
williamgilpin
pypdb

A Python API for the RCSB Protein Data Bank (PDB)

5K 336 76
compomics
deeplc

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.

4K 75 24
the-omics-os
lobster-ai

The self-evolving agentic framework for bioinformatics

4K 31 6
the-omics-os
lobster-ai-tui

The self-evolving agentic framework for bioinformatics

4K 31 6
compomics
psm-utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python

4K 31 10
uclahs-cds
mopepgen

Multi-Omics Peptide Generator

3K 30 5
bigbio
sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

3K 32 29
MannLabs
alphastats

An open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics

2K 87 17
MannLabs
directlfq

Fast and accurate label-free quantification for small and very large numbers of proteomes

2K 61 7
MannLabs
peptdeep

Deep learning framework for proteomics

2K 152 26
PRIDE-Archive
pridepy

Python Client library for PRIDE Rest API

2K 40 9
wfondrie
mokapot

Fast and flexible semi-supervised learning for peptide detection in Python

2K 51 20
MannLabs
alphadia

A novel proteomics search engine for DIA data based on end-to-end transfer learning.

2K 108 11
hgb-bin-proteomics
pyxlms

A python package to process protein cross-linking data.

2K 4 2
CompOmics
im2deep

Collisional cross-section prediction for modified and multiconformational peptides

2K 13 2
compomics
ms2rescore

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications.

2K 64 21
wilhelm-lab
spectrum-fundamentals

Fundamental functions, annotation pipeline and constants for oktoberfest

1K 13 2
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