proteomics-data-analysis

There are 8 repositories under proteomics-data-analysis topic.

• 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.

  olinkproteomicsproteomics-data-analysisrrstats
  Language:R 121

• fgcz / prolfqua

  Differential Expression Analysis tool box R lang package for omics data

  proteomics-data-analysisrstats-packagehypothesis-testingquality-controlr-packagedifferential-expression-analysisprotein-quantification
  Language:R 46

• SomaLogic / SomaDataIO

  The SomaDataIO package loads and exports 'SomaScan' data via the 'SomaLogic Operating Co., Inc.' proprietary data file, called an ADAT ('*.adat'). The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.

  proteomics-data-analysisr-packagerproteomicssomascanadat
  Language:R 28

• SlavovLab / DO-MS

  An modular and extensible app for visualization of mass spectrometry data and optimization of data acquisition.

  mass-spectrometryproteomicsproteomics-data-analysissingle-cellsingle-page-applicationsvisulization
  Language:R 27

• tbaccata / amica

  amica: an interactive and user-friendly web-based platform for the analysis of proteomics data

  proteomicsproteomics-data-analysismaxquantfragpipeshiny-r
  Language:R 27

• bigbio / sdrf-pipelines

  `sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files

  multiomicsmsstatssdrfproteomics-data-analysisproteomicsmass-spectrometrymaxquantopenms
  Language:Python 26
• VolcaNoseR

  JoachimGoedhart / VolcaNoseR

  Shiny app for making and annotating Volcano plots

  volcanoggplot2shinyappshinyproteomics-data-analysisgenomic-data-analysisdataviz
  Language:R 25
• HistoJS

  Mmasoud1 / HistoJS

  HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

  cell-cell-interactioncell-segmentationmibiscopemultiplexed-imagingmultiplexed-imaging-analysisome-tiffphenotypingproteomicsproteomics-data-analysissingle-cellwhole-slide-imagingdigital-slide-archiveimage-processingmultichannelspatial-biologyspatial-data-analysis
  Language:JavaScript 23

• nwamsley1 / Pioneer.jl

  CLI toolkit for fast analysis of DIA proteomics experiments and in silico library prediction

  mass-spectrometryproteomics-data-analysis
  Language:Julia 19

• SlavovLab / plexDIA

  Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.

  high-throughputmass-spectrometryproteomics-data-analysissingle-cellmultiplexedplexdia
  Language:R 12

• SlavovLab / SCP_recommendations

  Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments. The code is distributed under an MIT license.

  benchmark-frameworkbenchmarkingcommunity-projectproteomicsproteomics-data-analysissingle-cell
  Language:R 12
• autoprot

  ag-warscheid / autoprot

  autoprot provides standardised, fast, and reliable proteomics data analysis while ensuring a high customisability needed to tailor the analysis pipeline to specific experimental strategies.

  mass-spectrometryproteomics-data-analysispythonr
  Language:Python 10

• buenoalvezm / Pan-cancer-profiling

  This repository contains the code to reproduce our exploratory analysis of a pan-cancer plasma proteomics dataset, including differential expression analysis and disease classification (https://doi.org/10.1038/s41467-023-39765-y). The data can be explored in the Human Protein Atlas: www.proteinatlas.org/humanproteome/disease.

  disease-classificationpan-cancer-analysisproteomics-data-analysis
  Language:R 10

• hds-sandbox / proteomics-sandbox

  A resource for biomedical students and researchers. Includes proteomics software tools like FragPipe, MaxQuant, PDV, SearchGUI, ThermoRawFileParser, and PeptideShaker. Offers a user-friendly interface, automated identification and quantification, comprehensive data analysis, and lightweight clone feature for optimized storage.

  biomedical-researchcomputational-biologydata-analysisdata-visualizationdataset-managementproteomicsproteomics-data-analysisuser-friendly-interfaceclinical-proteomicslightweight-cloningproteomics-software
  Language:Jupyter Notebook 10

• cox-labs / CoxLab_Bug_Reporting

  MaxQuant and Perseus Bug Reporting

  bugbugreportsbioinformaticsbioinformatics-analysisproteomicsproteomics-dataproteomics-data-analysis
  9

• breimanntools / xomics

  Python framework for explainable omics analysis

  data-integrationdifferential-gene-expressionexplainablemissing-value-imputationomicsproteomics-data-analysis
  Language:Jupyter Notebook 7

• wulongict / SpectralArchive

  Visualization of spectral archive

  opensearchproteomics-data-analysisreal-timevisualization
  Language:C++ 7

• SlavovLab / QuantQC

  QuantQC is a package for quality control (QC) of single-cell proteomics data. It is optimized to work with nPOP, a method for massively parallel sample preparation on glass slides.

  mass-spectrometryomicsproteomiproteomics-data-analysisquality-controlsample-preparationsingle-cell-analysissingle-cell-omics
  Language:HTML 6

• moritzmadern / Cassiopeia_LFQ

  R script to perform standard analysis steps for label-free proteomics data

  label-freeproteomicsproteomics-data-analysis
  5

• SomaLogic / SomaScan.db

  An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc.

  adatbioconductor-packageproteomicsproteomics-data-analysisrr-packagesomascan
  Language:R 5

• symbioticMe / batch_effects_workflow_code

  Code accompanying batch effects processing workflow for "omic" data, mainly targeted for proteomics

  batch-effectsproteomics-data-analysisnormalization
  Language:R 5

• czbiohub-sf / grassp

  GRaph-based Analysis of Subcellular/Spatial Proteomics

  anndataproteomics-data-analysisscanpyspatial-proteomicssubcellular-localization
  Language:Python 4

• MateuszFido / LCMSpector

  📊 User-friendly mass spectrometry and chromatography data analysis app with native UI, graphing, quantification, MS/MS and data export capabilities

  analytical-chemistryliquid-chromatographymass-spectrometrymetabolomicslc-msdatadata-analysisanalyzedata-scienceglycomicsproteomicsproteomics-data-analysismzmlmzml-filesopen-source
  Language:Python 4

• dev-ev / isobaric-inspection-jupyter

  Inspecting the quality of isobaric labeling proteomic data in a Jupyter notebook. Data output from Proteome Discoverer.

  data-qualitydata-visualizationdata-wranglingisobaric-labelingjupyterlabmass-spectrometryproteome-discovererproteomicsproteomics-data-analysispythonquantitative-proteomics
  Language:Jupyter Notebook 3

• MiguelCos / Fragterminomics

  Annotation and processing of peptides from FragPipe search results

  analysisrrstatsproteolytic-enzymesproteomics-data-analysisproteomics-data-integrationproteolysis
  Language:R 3
• ProteinCleaverStreamlitApp

  pgarrett-scripps / ProteinCleaverStreamlitApp

  Protein Cleaver is a versatile tool for protein analysis and digestion.

  digestionfastamass-spectrometrypeptidepeptide-identificationpeptide-sequencespeptidesproteinprotein-sequencesproteomicsproteomics-data-analysisstreamlitstreamlit-cloud
  Language:Python 3

• russelllab / wesa

  WeSA (Weighted SocioAffinity): a tool for improving affinity proteomics data.

  flask-applicationprotein-protein-interactionproteomics-data-analysisvisualization
  Language:HTML 3

• SlavovLab / CellPermeability

  Cell Permeability analysis

  mass-spectrometryproteomicsproteomics-data-analysisqcsingle-cellsingle-cell-analysis
  Language:R 3

• SlavovLab / HIquant

  HIquant: An algorithm for quantifying homologous proteins and proteoforms from bottom-up mass-spec data

  inferencemass-spectrometryproteoformsproteomicsproteomics-data-analysis
  Language:Python 3

• SomaLogic / SomaPlotr

  A highly specialized suite of standardized plotting routines based on the "Grammar of Graphics" framework of mapping variables to aesthetics used in 'ggplot2'. Graphics types are biased towards visualizing SomaScan (proteomic) data.

  datavizggplot2proteomicsproteomics-data-analysisrr-packagesomascan
  Language:R 3

• daisybio / PRONE.Shiny

  Code of the R Shiny App of the PRONE R Package.

  normalizationproteomics-data-analysisshinyapps
  Language:R 2

• lmboat / protein_structure_annotations

  Map residue numbers from experimental protein structures to primary protein sequences and calculate the relative solvent accessibility of each residue

  pdbprotein-mappingprotein-structureproteomicsproteomics-data-analysisuniprot
  Language:Python 2

• lmboat / residue_function_annotations

  Identify small-molecule sites of labeling that are annotated as active sites, binding sites, disulfide bonds and redox active sites

  protein-functionprotein-ligand-interactionsproteomicsproteomics-data-analysisuniprot
  Language:Jupyter Notebook 2

• SamueldelaCamaraFuentes / TraianProt

  R package and Shiny app for the dowstream analysis of quantitative proteomic data

  dia-nnmass-spectrometrymaxquantmsfraggerproteome-discovererproteomicsproteomics-data-analysis
  Language:R 2

• SlavovLab / Protein-Clearance

  Analysis from Leduc and Slavov (2025): Protein degradation and growth dependent dilution substantially shape mammalian proteomes

  gene-expressionproteinproteomics-data-analysisproteomics-datasetstissue-analysis
  Language:R 2

• vaishnavpvarma / vaxijen-antigenicity-parser

  Automated parser for VaxiJen output 🚀 A lightweight Perl tool to extract and tabulate antigenicity predictions from VaxiJen . Designed for bioinformatics, immunoinformatics, and reverse vaccinology workflows, this script helps researchers process large datasets into clean, ready-to-analyze tables.

  bioinformaticscomputational-biologyexcel-converterfastaimmunoinformaticsimmunologyperl-scriptproteomicsproteomics-data-analysisvaccine-developmentantigenicity-predictionpeptide-analysisvaxijen
  Language:Perl 2