proteomics
There are 636 repositories under proteomics topic.
OpenMS/OpenMS
The codebase of the OpenMS project
williamgilpin/pypdb
A Python API for the RCSB Protein Data Bank (PDB)
tariqdaouda/pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
galaxyproject/training-material
A collection of Galaxy-related training material
lightdock/lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
lazear/sage
Proteomics search & quantification so fast that it feels like magic
Nesvilab/FragPipe
A cross-platform proteomics data analysis suite
lgatto/TeachingMaterial
Various teaching material
MannLabs/alphapept
A modular, python-based framework for mass spectrometry. Powered by nbdev.
soedinglab/plass
sensitive and precise assembly of short sequencing reads
refresh-bio/FAMSA
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
lgatto/MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics
MannLabs/alphapeptdeep
Deep learning framework for proteomics
Nesvilab/philosopher
PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
Nesvilab/MSFragger
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
Olink-Proteomics/OlinkRPackage
Olink R package: A collection of functions to facilitate analysis of proteomic data from Olink. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.
mrzResearchArena/PyFeat
A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences
lgatto/RforProteomics
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
bigbio/proteomics-sample-metadata
The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
MannLabs/alphamap
An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
twoXes/awesome-structural-bioinformatics
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
wfondrie/depthcharge
A deep learning toolkit for mass spectrometry
SysBioChalmers/GECKO
Toolbox for including enzyme constraints on a genome-scale model.
MannLabs/alphapeptstats
Python Package for the downstream analysis of mass-spectrometry-based proteomics data
jpquast/protti
Picotti lab data analysis package.
saezlab/cosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
compomics/DeepLC
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
MannLabs/alphadia
modular & open DIA search
fraenkel-lab/OmicsIntegrator2
Prize-Collecting Steiner Forests for Interactomes
wheretrue/exon
Exon is an OLAP query engine specifically for biology and life science applications.
compomics/ms2rescore
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
Russel88/DAtest
Compare different differential abundance and expression methods
compomics/peptide-shaker
Interpretation of proteomics identification results
horsepurve/DeepRTplus
Deep (Transfer) Learning for Peptide Retention Time Prediction
ProteomicsML/ProteomicsML
Community-curated tutorials and datasets for ML in proteomics
wenbostar/PDV
PDV: an integrative proteomics data viewer