Topic: proteomics Goto Github

👇 Here are 599 public repositories matching this topic...

bigbio / proteomics-sample-metadata
proteomics,The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
Organization: bigbio
metadata sdrf pride-metadata proteomics msrun-metadata multiomics sdrf-proteomics proteomics-datasets proteomics-community proteomics-experiments

cbielow / ptxqc
proteomics,A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant
User: cbielow
maxquant quality-control report metric proteomics heatmap match-between-runs drag-and-drop openms mztab

compomics / deeplc
proteomics,DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
Organization: compomics
Home Page: https://iomics.ugent.be/deeplc
proteomics peptides retention-time peptide-modification deep-learning

compomics / ms2pip
proteomics,MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
Organization: compomics
Home Page: https://ms2pip.readthedocs.io
machine-learning mass-spectrometry peptide-identification proteomics spectrum-prediction peptide-spectrum

compomics / ms2rescore
proteomics,Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
Organization: compomics
Home Page: https://ms2rescore.readthedocs.io
proteomics ms2pip percolator deeplc peptide-identification

compomics / peptide-shaker
proteomics,Interpretation of proteomics identification results
Organization: compomics
Home Page: http://compomics.github.io/projects/peptide-shaker.html
proteomics protein-identification bioinformatics java

compomics / searchgui
proteomics,Highly adaptable common interface for proteomics search and de novo engines
Organization: compomics
Home Page: http://compomics.github.io/projects/searchgui.html
proteomics protein-identification bioinformatics java

fraenkel-lab / omicsintegrator2
proteomics,Prize-Collecting Steiner Forests for Interactomes
Organization: fraenkel-lab
Home Page: https://fraenkel-lab.github.io/OmicsIntegrator2
omics proteomics prize-collecting steiner-tree

galaxyproject / training-material
proteomics,A collection of Galaxy-related training material
Organization: galaxyproject
Home Page: https://training.galaxyproject.org
usegalaxy training materials ngs tutorial metagenomics proteomics rnaseq chip-seq hacktoberfest

horsepurve / deeprtplus
proteomics,Deep (Transfer) Learning for Peptide Retention Time Prediction
User: horsepurve
deep-learning bioinformatics proteomics analytical-chemistry peptides capsule-network

johon-lituobang / md
proteomics,Matrix dissimilarity from the differences of Moments and sparsity
User: johon-lituobang
Home Page: https://doi.org/10.5281/zenodo.10406288
dissimilarity dissimilarity-matrix dissimilarity-measures genome genomics matrix metabolome microbiome omics omics-analysis

jpquast / protti
proteomics,Picotti lab data analysis package.
User: jpquast
Home Page: https://jpquast.github.io/protti/
r proteomics mass-spectrometry data-analysis systems-biology lip-ms omics protein

lazear / sage
proteomics,Proteomics search & quantification so fast that it feels like magic
User: lazear
Home Page: https://sage-docs.vercel.app
bioinformatics proteomics mass-spectrometry

lgatto / msnbase
proteomics,Base Classes and Functions for Mass Spectrometry and Proteomics
User: lgatto
Home Page: http://lgatto.github.io/MSnbase/
bioconductor mass-spectrometry r proteomics bioinformatics proteomics-data visualisation

lgatto / rforproteomics
proteomics,Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
User: lgatto
Home Page: http://lgatto.github.io/RforProteomics
bioconductor bioconductor-packages proteomics-data r proteomics mass-spectrometry tutorial

lgatto / teachingmaterial
proteomics,Various teaching material
User: lgatto
Home Page: http://lgatto.github.io/TeachingMaterial/
r programming-tutorial oo-programming data-analysis teaching-materials statistics vectorisation proteomics visualisation make

lightdock / lightdock
proteomics,Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Organization: lightdock
Home Page: https://lightdock.org/
protein protein-structure protein-protein-interaction protein-docking swarm-intelligence glowworm-swarm-optimization protein-dna-interactions peptides dna docking

mannlabs / alphadia
proteomics,modular & open DIA search
Organization: mannlabs
Home Page: https://alphadia.readthedocs.io
bioinformatics mass-spectrometry open-source peptide-identification proteomics

mannlabs / alphamap
proteomics,An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
Organization: mannlabs
Home Page: https://mannlabs.github.io/alphamap/
mass-spectrometry proteomics peptide-level visualization python gui

mannlabs / alphapept
proteomics,A modular, python-based framework for mass spectrometry. Powered by nbdev.
Organization: mannlabs
Home Page: https://mannlabs.github.io/alphapept/
alphapept-ecosystem bioinformatics mass-spectrometry proteomics

mannlabs / alphapeptdeep
proteomics,Deep learning framework for proteomics
Organization: mannlabs
deep-learning hla machine-learning proteomics python

mannlabs / alphapeptstats
proteomics,Python Package for the downstream analysis of mass-spectrometry-based proteomics data
Organization: mannlabs
Home Page: https://alphapeptstats.readthedocs.io/en/latest/
mass-spectrometry maxquant proteomics alphapept-ecosystem dia-nn fragpipe msfragger spectronaut

mannlabs / directlfq
proteomics,Fast and accurate label-free quantification for small and very large numbers of proteomes
Organization: mannlabs
Home Page: https://doi.org/10.1101/2023.02.17.528962
algorithms alphapept-ecosystem bioinformatics proteomics python quantification

metaboverse / metaboverse
proteomics,Visualization and analysis platform for metabolic data and network pattern recognition
Organization: metaboverse
Home Page: https://metaboverse.readthedocs.io/en/latest
metabolism pattern-recognition reaction chemical d3 metabolomics network networkx proteomics sequencing

mikelkou / fava
proteomics,Functional Associations using Variational Autoencoders
User: mikelkou
single-cells co-expression deep-learning networks networks-biology proteomics

mrzresearcharena / pyfeat
proteomics,A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences
User: mrzresearcharena
Home Page: http://rafsanjani.pythonanywhere.com/
computational-biology bioinformatics genomics proteomics

nesvilab / fragpipe
proteomics,A cross-platform proteomics data analysis suite
Organization: nesvilab
Home Page: http://fragpipe.nesvilab.org
mass-spectrometry proteomics gui command-line-interface data-dependent-acquisition data-independent-acquisition isobaric-quantification label-free-quantification

nesvilab / msfragger
proteomics,Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
Organization: nesvilab
Home Page: https://msfragger.nesvilab.org
proteomics mass-spectrometry database-search bioinformatics

nesvilab / philosopher
proteomics,PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
Organization: nesvilab
Home Page: https://philosopher.nesvilab.org
bioinformatics proteomics mass-spectrometry ms-data go data-analysis

olink-proteomics / olinkrpackage
proteomics,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.
Organization: olink-proteomics
olink proteomics proteomics-data-analysis r rstats

openms / openms
proteomics,The codebase of the OpenMS project
Organization: openms
Home Page: https://www.openms.de
3-clause-bsd algorithms analyses c-plus-plus hacktoberfest linux macos mass-spectrometry metabolomics ms-data openms proteomics windows

pathwayanddataanalysis / causalpath
proteomics,A project for exploring differentially active signaling paths related to proteomics datasets
Organization: pathwayanddataanalysis
computational-biology bioinformatics proteomics phosphoproteomics causality-analysis pathway-analysis pathways

pfindstudio / pdeep
proteomics,pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning
Organization: pfindstudio
mass-spectrometry proteomics deep-learning

proteomicsml / proteomicsml
proteomics,Community-curated tutorials and datasets for ML in proteomics
Organization: proteomicsml
Home Page: https://www.proteomicsml.org
datasets machine-learning mass-spectrometry proteomics tutorials

pwilmart / paw_pipeline
proteomics,A Comet-based, best practices proteomics pipeline.
User: pwilmart
comet protein-identification protein-inference proteomics python3 tmt

refresh-bio / famsa
proteomics,Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
Organization: refresh-bio
bioinformatics guide-tree longest-common-subsequence multiple-sequence-alignment pfam proteomics sequence-similarity

rformassspectrometry / spectra
proteomics,Low level infrastructure to handle MS spectra
Organization: rformassspectrometry
Home Page: https://rformassspectrometry.github.io/Spectra/
rstats mass-spectrometry proteomics metabolomics bioconductor

russel88 / datest
proteomics,Compare different differential abundance and expression methods
User: russel88
microbiome rnaseq relative-abundances compare-methods differential-abundance-methods otu marker-gene-analysis 16s proteomics metabolomics

saezlab / cosmosr
proteomics,COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
Organization: saezlab
Home Page: https://saezlab.github.io/cosmosR/
metabolomic-data proteomics phosphoproteomics data-integration transcriptomics network-modelling

sheynkman-lab / long-read-proteogenomics
proteomics,A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
Organization: sheynkman-lab
pipeline proteomics long-read-sequencing isoforms nextflow

soedinglab / plass
proteomics,sensitive and precise assembly of short sequencing reads
Organization: soedinglab
Home Page: https://plass.mmseqs.com
bioinformatics metagenomics sequence-assembler proteins opensource proteomics metatranscriptomics

sysbiochalmers / gecko
proteomics,Toolbox for including enzyme constraints on a genome-scale model.
Organization: sysbiochalmers
Home Page: http://sysbiochalmers.github.io/GECKO/
proteomics data-integration toolbox matlab kinetics enzyme-constraints systems-biology

tariqdaouda / pygeno
proteomics,Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
User: tariqdaouda
Home Page: http://pygeno.iric.ca
bioinformatics biology genomics proteomics genome genome-annotation genome-browser genome-sequencing genomes medical

twoxes / awesome-structural-bioinformatics
proteomics,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.
User: twoxes
molecular-informatics chemistry machine-learning deep-learning cheminformatics biology quantum-chemistry docking protein alphafold

ursgal / ursgal
proteomics,Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis
Organization: ursgal
proteomics peptide-identification python mass-spectrometry ms-data proteomics-data mzml omics

wenbostar / pdv
proteomics,PDV: an integrative proteomics data viewer
User: wenbostar
proteomics proteogenomics msms visulization bioinformatics spectra-visualization psm

wfondrie / depthcharge
proteomics,A deep learning toolkit for mass spectrometry
User: wfondrie
Home Page: https://wfondrie.github.io/depthcharge/
deep-learning framework mass-spectrometry metabolomics proteomics pytorch

wfondrie / mokapot
proteomics,Fast and flexible semi-supervised learning for peptide detection in Python
User: wfondrie
Home Page: https://mokapot.readthedocs.io
proteomics machine-learning bioinformatics python conda peptide-detection percolator

wheretrue / exon
proteomics,Exon is an OLAP query engine specifically for biology and life science applications.
Organization: wheretrue
Home Page: https://www.wheretrue.dev/docs/exon/
arrow bioinformatics proteomics rust datafusion ngs sql

williamgilpin / pypdb
proteomics,A Python API for the RCSB Protein Data Bank (PDB)
User: williamgilpin
pdb blast proteomics protein-structure protein-sequences proteins protein-data-bank