proteomics

There are 30 repositories under proteomics topic.

OpenMS / OpenMS
The codebase of the OpenMS project
3-clause-bsd algorithms analyses c-plus-plus hacktoberfest linux macos mass-spectrometry metabolomics ms-data openms proteomics windows
Language:C++ 471
pyGeno
tariqdaouda / pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
bioinformatics biology genomics proteomics genome genome-annotation genome-browser genome-sequencing genomes medical medicine cancer cancer-genomics cancer-genomes ensembl gtf vcf snps csv-parser bed
Language:Python 309
williamgilpin / pypdb
A Python API for the RCSB Protein Data Bank (PDB)
pdb blast proteomics protein-structure protein-sequences proteins protein-data-bank
Language:Python 302
training-material
galaxyproject / training-material
A collection of Galaxy-related training material
usegalaxy training materials ngs tutorial metagenomics proteomics rnaseq chip-seq hacktoberfest
Language:HTML 297
lightdock
lightdock / lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
protein protein-structure protein-protein-interaction protein-docking swarm-intelligence glowworm-swarm-optimization protein-dna-interactions peptides dna docking artificial-intelligence protein-design proteomics structural-biology structural-bioinformatics bioinformatics bioinformatics-tool chemistry molecular-biology molecular-structures
Language:Python 297
sage
lazear / sage
Proteomics search & quantification so fast that it feels like magic
bioinformatics mass-spectrometry proteomics
Language:Rust 204
lgatto / TeachingMaterial
Various teaching material
r programming-tutorial oo-programming data-analysis teaching-materials statistics vectorisation proteomics visualisation make makefile
Language:HTML 179
Nesvilab / FragPipe
A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
mass-spectrometry proteomics search-engine pipeline gui
Language:Java 179
MannLabs / alphapept
A modular, python-based framework for mass spectrometry. Powered by nbdev.
alphapept-ecosystem bioinformatics mass-spectrometry proteomics
Language:HTML 166
refresh-bio / FAMSA
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
bioinformatics guide-tree longest-common-subsequence multiple-sequence-alignment pfam proteomics sequence-similarity
Language:C 139
plass
soedinglab / plass
sensitive and precise assembly of short sequencing reads
bioinformatics metagenomics sequence-assembler proteins opensource proteomics metatranscriptomics
Language:C 132
lgatto / MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics
bioconductor mass-spectrometry r proteomics bioinformatics proteomics-data visualisation
Language:R 123
philosopher
Nesvilab / philosopher
PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
bioinformatics proteomics mass-spectrometry ms-data go data-analysis
Language:Go 109
MannLabs / alphapeptdeep
Deep learning framework for proteomics
deep-learning hla machine-learning proteomics python
Language:Jupyter Notebook 102
Nesvilab / MSFragger
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
proteomics mass-spectrometry database-search bioinformatics
Language:HTML 99
PyFeat
mrzResearchArena / PyFeat
A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences
bioinformatics computational-biology genomics proteomics
Language:Python 90
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.
olink proteomics proteomics-data-analysis r rstats
Language:R 83
lgatto / RforProteomics
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
bioconductor bioconductor-packages proteomics-data r proteomics mass-spectrometry tutorial
Language:TeX 82
bigbio / proteomics-sample-metadata
The Proteomics Experimental Design file format: Standard for experimental design annotation
mage-tab metadata msrun-metadata multiomics pride-metadata proteomexchange proteomics proteomics-community proteomics-datasets proteomics-experiments sdrf sdrf-proteomics
Language:Python 75
MannLabs / alphamap
An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
mass-spectrometry proteomics peptide-level visualization python gui
Language:Jupyter Notebook 74
SysBioChalmers / GECKO
Toolbox for including enzyme constraints on a genome-scale model.
proteomics data-integration toolbox matlab kinetics enzyme-constraints systems-biology
Language:MATLAB 64
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.
molecular-informatics chemistry machine-learning deep-learning cheminformatics biology quantum-chemistry docking protein alphafold protein-structure-prediction awesome-list bioinformatics bioinformatics-pipeline bioinformatics-analysis proteomics genomics genetics genome-alignment protein-structure
Language:Python 60
jpquast / protti
Picotti lab data analysis package.
data-analysis lip-ms mass-spectrometry omics protein proteomics r systems-biology
Language:R 57
depthcharge
wfondrie / depthcharge
A deep learning toolkit for mass spectrometry
deep-learning framework mass-spectrometry metabolomics proteomics pytorch
Language:Python 57
saezlab / cosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
metabolomic-data proteomics phosphoproteomics data-integration transcriptomics network-modelling
Language:R 54
MannLabs / alphapeptstats
Python Package for the downstream analysis of mass-spectrometry-based proteomics data
alphapept-ecosystem dia-nn fragpipe mass-spectrometry maxquant msfragger proteomics spectronaut
Language:Jupyter Notebook 52
fraenkel-lab / OmicsIntegrator2
Prize-Collecting Steiner Forests for Interactomes
omics proteomics prize-collecting steiner-tree
Language:Jupyter Notebook 51
horsepurve / DeepRTplus
Deep (Transfer) Learning for Peptide Retention Time Prediction
deep-learning bioinformatics proteomics analytical-chemistry peptides capsule-network
Language:Python 50
compomics / DeepLC
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
deep-learning peptide-modification peptides proteomics retention-time
Language:Python 49
Russel88 / DAtest
Compare different differential abundance and expression methods
microbiome rnaseq relative-abundances compare-methods differential-abundance-methods otu marker-gene-analysis 16s proteomics metabolomics metagenomics differential-expression auc false-positive-control
Language:R 48
compomics / peptide-shaker
Interpretation of proteomics identification results
bioinformatics java protein-identification proteomics
Language:Java 47
wenbostar / PDV
PDV: an integrative proteomics data viewer
proteomics proteogenomics msms visulization bioinformatics spectra-visualization psm
Language:Java 43
cbielow / PTXQC
A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant
maxquant quality-control report metric proteomics heatmap match-between-runs drag-and-drop openms mztab quality-metrics hacktoberfest
Language:HTML 42
ursgal / ursgal
Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis
proteomics peptide-identification python mass-spectrometry ms-data proteomics-data mzml omics
Language:Python 42
ProteomicsML / ProteomicsML
Community-curated tutorials and datasets for ML in proteomics
datasets machine-learning mass-spectrometry proteomics tutorials
Language:Jupyter Notebook 41
tubanlee / MD
Matrix dissimilarity from the differences of Moments and sparsity
dissimilarity dissimilarity-matrix dissimilarity-measures genome genomics matrix metabolome microbiome omics omics-analysis omics-data-analysis proteome proteomics microbiomics
Language:R 40