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 83

• 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 36

• 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:HTML 23

• 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 22

• tbaccata / amica

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

  proteomicsproteomics-data-analysismaxquantfragpipeshiny-r
  Language:R 20
• VolcaNoseR

  JoachimGoedhart / VolcaNoseR

  Shiny app for making and annotating Volcano plots

  volcanoggplot2shinyappshinyproteomics-data-analysisgenomic-data-analysisdataviz
  Language:R 19
• 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 15

• bigbio / sdrf-pipelines

  A repository to convert SDRF proteomics files into pipelines config files

  multiomicsmsstatssdrfproteomics-data-analysisproteomicsmass-spectrometry
  Language:Python 14

• 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 9
• 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 6

• breimanntools / xomics

  Python framework for explainable omics analysis

  data-integrationdifferential-gene-expressionexplainablemissing-value-imputationomicsproteomics-data-analysis
  Language:Jupyter Notebook 6

• 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 6

• cox-labs / CoxLab_Bug_Reporting

  MaxQuant and Perseus Bug Reporting

  bugbugreportsbioinformaticsbioinformatics-analysisproteomicsproteomics-dataproteomics-data-analysis
  6

• 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:Dockerfile 6

• 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 6

• moritzmadern / Cassiopeia_LFQ

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

  label-freeproteomicsproteomics-data-analysis
  5

• wulongict / SpectralArchive

  Visualization of spectral archive

  opensearchproteomics-data-analysisreal-timevisualization
  Language:C++ 5
• 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 4

• dev-ev / isobaric-inspection-jupyter

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

  pythondata-visualizationjupyterlabproteomicsproteomics-data-analysismass-spectrometrydata-wranglingdata-qualityproteome-discovererisobaric-labelingquantitative-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

• dev-ev / isobaric-correlations

  Exploring correlations in an isobaric labeling mass spectrometry-based proteomic data set

  proteomicsproteomics-data-analysiscorrelation-matrixescherichia-colipearson-correlation-coefficientisobaric-quantificationtmt-data-analysis
  Language:Jupyter Notebook 2

• dev-ev / julia-vs-python-ms-scripting

  Performance of Julia and Python for reading and matching mass spectrometry data

  juliapythonnumpymass-spectrometryproteomics-data-analysisperformance-testingbenchmarking
  Language:Jupyter Notebook 2

• jessmhoehner / Methods

  Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

  deseq2edgerbayseqrnaseqphyloseq16smicrobiome-analysisproteomics-data-analysisproteusldmqvaluermetabolomicsmetagenomicstranscriptomics-data
  Language:R 2

• SlavovLab / HIquant

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

  inferencemass-spectrometryproteoformsproteomicsproteomics-data-analysis
  Language:Python 2

• 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 2

• symbioticMe / batch_effects_workflow_code

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

  batch-effectsproteomics-data-analysisnormalization
  Language:R 2

• bibs-lab / SpecGlobX

  SpecGlobX: java program that can be used when interpreting mass spectra in proteomics.

  proteomics-data-analysismassspectra
  Language:Java 1

• chinmayaNK22 / R_Scripts

  Routinely used R scripts in statistical analysis of proteomic experiment results with figure and plot generation

  plottingproteomics-data-analysisrscript
  Language:R 1

• loankimrobinson / loankimrobinson.github.io

  This is Loan Robinson Github Page, which includes all tutorials for education purpose.

  clinical-researchclinical-trialsgenomejupyter-notebookmachine-learningngs-analysisobservational-studypythonpythonlibrariesrna-seq-analysisrshinydashboardrstudioshell-scriptingadverse-eventsproteomics-data-analysistranscriptomics
  Language:HTML 1

• moritzmadern / InterferenceModeling_in_MultiplexProteomics

  Workflow to perform interference modeling and interference correction for MS2-based multiplex proteomics data

  algorithmisobaric-labelingproteomicsproteomics-data-analysis
  Language:R 1

• russelllab / wesa

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

  flask-applicationprotein-protein-interactionproteomics-data-analysisvisualization
  Language:HTML 1

• SamueldelaCamaraFuentes / Downstreaming-analysis-workflow

  Pipeline and shiny app for the downstreaming analysis of quantitative proteomic data

  dia-nnmaxquantmsfraggermass-spectrometryproteomicsproteomics-data-analysis
  Language:R 1

• seanyoon777 / proteomics_project

  Data analysis on relationship between neurodegenerative diseases and plasma/CSF protein expression levels.

  alzheimer-disease-diagnosticsbioinformaticsproteomics-data-analysis
  Language:R 1

• seerbio / seer-pas-sdk

  Python SDK for Seer PAS

  proteomicsproteomics-data-analysispython-sdk
  Language:Python 1

• sivkri / Perseus-MS-Proteomics-Venn

  Mass spectrometry Perseus Data analysis

  data-analysismass-spectrometryperseusproteomicsproteomics-dataproteomics-data-analysisproteomics-data-integration
  Language:Jupyter Notebook 1

• 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 1