Repositories list

• MSstatsShiny

  Public
  R-Shiny GUI integrated with the MSstats package family

  R

  •1010 forks•2020 stars•1515 issues•33 pull requests•Updated Apr 24, 2026Apr 24, 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

  •22 forks•1414 stars•1010 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• MSstats

  Public
  R package - MSstats

  R

  •

  Other

  •5252 forks•9797 stars•1515 issues•44 pull requests•Updated Apr 24, 2026Apr 24, 2026

• MSstatsConvert

  Public
  Converter functions for the MSstats package

  data-importproteomicsmass-spectrometry+ 1

  data-importproteomicsmass-spectrometrymsstats

  R

  •55 forks•1111 stars•55 issues•11 pull request•Updated Apr 24, 2026Apr 24, 2026

• Causomic

  Public
  Causal inference methods for -omics research

  proteomicsbayesian-inferenceomics+ 2

  proteomicsbayesian-inferenceomicscausal-inferencecausal-ai

  Jupyter Notebook

  •33 forks•22 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• MSstatsResponse

  Public
  R

  •11 fork•11 star•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• MSstatsBioNet

  Public
  R

  •

  Other

  •00 forks•22 stars•22 issues•1212 pull requests•Updated Apr 21, 2026Apr 21, 2026

• 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

  •1515 forks•3131 stars•1111 issues•44 pull requests•Updated Apr 16, 2026Apr 16, 2026

• MSstatsBig

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

  R

  •11 fork•22 stars•22 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• MSstatsLiP

  Public
  HTML

  •22 forks•77 stars•44 issues•11 pull request•Updated Apr 7, 2026Apr 7, 2026

• MSstatsWeightedSummary

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

  R

  •

  GNU General Public License v3.0

  •11 fork•11 star•33 issues•00 pull requests•Updated Mar 20, 2026Mar 20, 2026

• MSstatsResponse-Manuscript

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 5, 2026Mar 5, 2026

• .github

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 11, 2026Feb 11, 2026

• MSIreg-vignettes

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

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 6, 2023Oct 6, 2023

• MSstatsTracker

  Public
  Simple Shiny apps for displaying MSstats Ecosystem usage statistics

  R

  •00 forks•00 stars•00 issues•00 pull requests•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

  •22 forks•66 stars•11 issue•11 pull request•Updated Jun 16, 2023Jun 16, 2023

• MSstats_benchmarking

  Public
  Benchmarking MSstats against the most popular proteomics statistical analysis methods

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 23, 2023Apr 23, 2023

• Cardinal3-vignettes

  Public
  Vignettes for Cardinal3 paper

  HTML

  •

  MIT License

  •33 forks•1010 stars•00 issues•00 pull requests•Updated Feb 20, 2023Feb 20, 2023

• MSstatsPTM-manuscript

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•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

  •22 forks•33 stars•11 issue•00 pull requests•Updated Oct 23, 2021Oct 23, 2021

• SharedPeptidesApp

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 12, 2021Feb 12, 2021

• MSstatsGlycans

  Public
  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 27, 2021Jan 27, 2021

• MSstats_testing

  Public
  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 29, 2020Sep 29, 2020

• mi-CNN_MSI

  Public
  R

  •00 forks•44 stars•11 issue•00 pull requests•Updated Jul 5, 2020Jul 5, 2020

• MSstatsSampleSize-Shiny

  Public
  Shiny for MSstatsSampleSize R package

  R

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jun 15, 2020Jun 15, 2020

• IonSpattern

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 11, 2019Mar 11, 2019