Repositories list

• MSstatsShiny

  Public
  R-Shiny GUI integrated with the MSstats package family

  R

  •10•20•21•3•Updated Mar 13, 2026Mar 13, 2026

• MSstatsResponse

  Public
  HTML

  •1•1•0•2•Updated Mar 13, 2026Mar 13, 2026

• MSstats

  Public
  R package - MSstats

  R

  •

  Other

  •50•92•16•3•Updated Mar 13, 2026Mar 13, 2026

• MSstatsBioNet

  Public
  R

  •

  Other

  •0•2•2•1•Updated Mar 11, 2026Mar 11, 2026

• MSstatsResponse-Manuscript

  Public
  R

  •0•0•0•0•Updated Mar 5, 2026Mar 5, 2026

• MSstatsLiP

  Public
  HTML

  •2•7•4•1•Updated Mar 5, 2026Mar 5, 2026

• MSstatsConvert

  Public
  Converter functions for the MSstats package

  data-importproteomicsmass-spectrometry+ 1

  data-importproteomicsmass-spectrometrymsstats

  R

  •5•10•5•2•Updated Mar 3, 2026Mar 3, 2026

• MSstatsBig

  Public
  MSstats functionality to handle large DIA datasets. Replaces standard MSstats converters with MSstatsBig converters.

  R

  •0•2•1•0•Updated Mar 2, 2026Mar 2, 2026

• MSstatsPTM

  Public
  Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments

  proteomicspost-translational-modification

  proteomicspost-translational-modification

  R

  •

  Artistic License 2.0

  •2•13•10•0•Updated Feb 26, 2026Feb 26, 2026

• .github

  Public
  0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

• Causomic

  Public
  Causal inference methods for -omics research

  proteomicsbayesian-inferenceomics+ 2

  proteomicsbayesian-inferenceomicscausal-inferencecausal-ai

  Python

  •3•2•0•0•Updated Nov 18, 2025Nov 18, 2025

• MSstatsTMT

  Public
  R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

  proteomicslabelingmass-spectrometry+ 3

  proteomicslabelingmass-spectrometrymsstatstmttmt-data-analysis

  R

  •15•30•11•4•Updated Jul 28, 2025Jul 28, 2025

• MSstatsWeightedSummary

  Public
  An R package for shared peptides exploration in label-free and labeled MS experiments

  R

  •

  GNU General Public License v3.0

  •1•1•3•0•Updated May 20, 2025May 20, 2025

• MSIreg-vignettes

  Public
  Vignettes for installation instructions, case studies and performance metrics for the MSIreg application note.

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 6, 2023Oct 6, 2023

• MSstatsTracker

  Public
  Simple Shiny apps for displaying MSstats Ecosystem usage statistics

  R

  •0•0•0•0•Updated Jul 19, 2023Jul 19, 2023

• MSstatsSampleSize

  Public
  Simulation tool for optimal design of high-dimensional MS-based proteomics experiment

  proteomicsmass-spectrometryexperiment-design+ 1

  proteomicsmass-spectrometryexperiment-designmsstats

  R

  •2•5•1•1•Updated Jun 16, 2023Jun 16, 2023

• MSstats_benchmarking

  Public
  Benchmarking MSstats against the most popular proteomics statistical analysis methods

  R

  •0•0•0•0•Updated Apr 23, 2023Apr 23, 2023

• Cardinal3-vignettes

  Public
  Vignettes for Cardinal3 paper

  HTML

  •

  MIT License

  •3•10•0•0•Updated Feb 20, 2023Feb 20, 2023

• MSstatsPTM-manuscript

  Public
  R

  •0•0•0•0•Updated Aug 30, 2022Aug 30, 2022

• MSstatsLOBD

  Public
  R/Bioconductor package for limit of blanc (LOB) and limit of detection (LOD) estimation

  proteomicsmass-spectrometry

  proteomicsmass-spectrometry

  R

  •0•0•0•0•Updated Jan 28, 2022Jan 28, 2022

• MSstatsTMTPTM

  Public
  R-based package for detecting differencially abundant post translational modifications (PTM) in shotgun mass spectrometry-bsed proteomic experiments with tandem…

  proteomicsmass-spectrometrymsstats+ 1

  proteomicsmass-spectrometrymsstatspost-translational-modification

  R

  •2•3•1•0•Updated Oct 23, 2021Oct 23, 2021

• SharedPeptidesApp

  Public
  R

  •0•0•0•0•Updated Feb 12, 2021Feb 12, 2021

• MSstatsGlycans

  Public
  R

  •1•0•0•0•Updated Jan 27, 2021Jan 27, 2021

• MSstats_testing

  Public
  R

  •1•0•0•0•Updated Sep 29, 2020Sep 29, 2020

• mi-CNN_MSI

  Public
  R

  •0•4•1•0•Updated Jul 5, 2020Jul 5, 2020

• MSstatsSampleSize-Shiny

  Public
  Shiny for MSstatsSampleSize R package

  R

  •1•2•0•0•Updated Jun 15, 2020Jun 15, 2020

• IonSpattern

  Public
  R

  •0•0•0•0•Updated Mar 11, 2019Mar 11, 2019