Topic: proteomics Goto Github

👇 Here are 558 public repositories matching this topic...

bigbio / proteomics-sample-metadata
proteomics,The Proteomics Experimental Design file format: Standard for experimental design annotation
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 / moff
proteomics, A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Organization: compomics
mass-spectrometry proteomics apex-intensity-ms1

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

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 makefile

lightdock / lightdock
proteomics,Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Organization: lightdock
Home Page: https://lightdock.org/
artificial-intelligence bioinformatics bioinformatics-tool chemistry dna docking glowworm-swarm-optimization molecular-biology molecular-structures peptides protein protein-design protein-dna-interactions protein-docking protein-protein-interaction protein-structure proteomics structural-bioinformatics structural-biology swarm-intelligence

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/
mass-spectrometry bioinformatics proteomics alphapept-ecosystem

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 bioinformatics proteomics quantification alphapept-ecosystem python

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 Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
Organization: nesvilab
Home Page: http://fragpipe.nesvilab.org
mass-spectrometry proteomics search-engine pipeline gui

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

nf-core / proteomicslfq
proteomics,Proteomics label-free quantification (LFQ) analysis pipeline
Organization: nf-core
Home Page: https://nf-co.re/proteomicslfq
nf-core nextflow pipeline workflow proteomics label-free-quantification openms

obf / faldo
proteomics,Feature Annotation Location Description Ontology
Organization: obf
ontology uniprot biology genomics proteomics

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

omicera / omiclearn
proteomics,🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data
Organization: omicera
Home Page: http://OmicLearn.com
machine-learning proteomics biomarker-discovery omics bioinformatics

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

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
protein-identification proteomics comet protein-inference tmt python3

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 multiple-sequence-alignment proteomics longest-common-subsequence pfam guide-tree sequence-similarity

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

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 metagenomics differential-expression auc false-positive-control

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

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

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
Home Page: http://pdv.zhang-lab.org
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

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