Repositories list

• IP2_File_Transfer

  Public
  Giving some SSH credentials to a file server with the files of IP2, it will explore a given list of IP2 projects to get all RAW files and DTASelect files and tr…

  transferdtaselect-filesssh-credentials

  transferdtaselect-filesssh-credentials

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•11 pull request•Updated Apr 14, 2026Apr 14, 2026

• RawConverter

  Public
  RawConverter on proteomicsyates by the lab of John R. Yates III

  C#

  •

  Apache License 2.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Jan 12, 2025Jan 12, 2025

• PINT

  Public
  PINT is a new comprehensive web-based system to store, visualize, and query experimental proteomics data obtained under different experimental conditions and pr…

  pythondatabasewiki+ 11

  pythondatabasewikiproteinsannotationsdata-integrationuniprotprotein-quantificationpintexperimental-conditions+ 4

  Java

  •

  Apache License 2.0

  •11 fork•44 stars•11 issue•66 pull requests•Updated Aug 6, 2024Aug 6, 2024

• utilities

  Public
  General Java util classes used across different projects

  data-modelutility-libraryproteomics+ 1

  data-modelutility-libraryproteomicsproteomics-data

  Java

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•44 pull requests•Updated Aug 23, 2023Aug 23, 2023

• ProteinClusterQuant

  Public
  Protein Cluster Quant is a Java software for the analysis of complex proteomics samples (quantitative or not). It helps to reduce the redundancy of the peptide-…

  javaproteincytoscape+ 17

  javaproteincytoscapeproteomicsproteomics-datalabel-free-quantificationredundancysalvadorquantitative-analysisquantitation+ 10

  Python

  •33 forks•66 stars•00 issues•00 pull requests•Updated Aug 23, 2023Aug 23, 2023

• proteoform_dbIndex

  Public
  extension of dbIndex module to index proteoforms

  Java

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 23, 2023Aug 23, 2023

• QuantParser

  Public
  Parser for quantitative data from files created by Census software.

  parserparseproteomics+ 7

  parserparseproteomicsproteomics-datacensuslabel-free-quantificationquantitative-dataisotopologueisobaric-quantificationsanxot

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 16, 2023Jun 16, 2023

• dbIndex

  Public
  Indexing of FASTA files for searching peptide masses and sequences

  databaseindexingfasta+ 3

  databaseindexingfastaproteomicsproteomics-dataproteomics-datasets

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•11 pull request•Updated May 23, 2023May 23, 2023

• ProteinAccessibilityCalculator

  Public
  Based on Jmol, it calculates the surface accessibility of specific sites in a given protein. Optionally it measures the distances between specific atoms of spec…

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•11 pull request•Updated Apr 17, 2023Apr 17, 2023

• mokapot

  Public
  Fast and flexible semi-supervised learning for peptide detection in Python

  Python

  •

  Apache License 2.0

  •2121 forks•00 stars•00 issues•00 pull requests•Updated Feb 10, 2023Feb 10, 2023

• GlycoMSQuant

  Public
  This is a Java stand-alone tool for the quantitation of glyco sites. It calculates the proportion of different glyco-PTMs in a protein of interest. It supports …

  proteomicsglycoproteomicsglycosylation+ 1

  proteomicsglycoproteomicsglycosylationglycomsquant

  Java

  •

  Apache License 2.0

  •11 fork•33 stars•11 issue•00 pull requests•Updated Dec 21, 2022Dec 21, 2022

• pctsea-parent

  Public
  PCTSEA (Proteomics Cell Type Enrichment Analysis) is a tool designed to statistically determine which cell types are significatively enriched in an input set of…

  javabioinformaticsrna-seq+ 10

  javabioinformaticsrna-seqstatisticsrshinycellproteomicssingle-cellenrichment-analysiskolmogorov-smirnov+ 3

  Java

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 5, 2022Jan 5, 2022

• DTASelectParser

  Public
  Java parser for DTASelect output files

  parserparser-libraryproteomics+ 2

  parserparser-libraryproteomicsjavaparserdtaselect

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 11, 2021Aug 11, 2021

• CensusTMT2MSstatsTMT

  Public
  Converter from Census TMT output file to the input of MSstatsTMT

  converterproteomicsproteomics-data+ 3

  converterproteomicsproteomics-datacensusmsstatstmt

  Java

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 2, 2021Aug 2, 2021

• ViSEAGO_Shiny

  Public
  R

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 30, 2021Jul 30, 2021

• pcomplex

  Public
  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 27, 2021Jul 27, 2021

• luciphor_dtaselect_integrator

  Public
  Program that integrates results from Luciphor (PTM localization scoring algorithm) into DTASelect output files.

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•22 issues•00 pull requests•Updated Mar 4, 2021Mar 4, 2021

• DTASelect2MzId

  Public
  Data file format converter, from DTASelect-filter.txt files (output from DTASelect software) to mzIdentML version 1.1.0 and 1.2.0

  converterformat-convertermzidentml+ 3

  converterformat-convertermzidentmlhupo-psidtaselectdtaselect-filter-files

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•11 issue•00 pull requests•Updated Jul 20, 2020Jul 20, 2020

• Dilu

  Public
  C

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 8, 2019Oct 8, 2019

• PCQ_GUI

  Public
  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 5, 2019Sep 5, 2019

• P3

  Public
  The Protein-Protein Predictor (P3) is a software for the prediction of real protein-protein interactions in multiple-bait IP-MS experiments

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 28, 2019May 28, 2019

• rt2dtaselect

  Public
  Adds retention time to dtaselect output files, by reading it from ms2 (either in the local system or in a remote server)

  rtdtaselectdtaselect-filter-files+ 2

  rtdtaselectdtaselect-filter-filesms2retention-time

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 17, 2019Apr 17, 2019

• DTASelect2PepXML

  Public
  Converter from DTASelect to pepXML formats

  spectrumconverterproteomics+ 7

  spectrumconverterproteomicstppproteomics-datadata-conversionpeptidespepxmldtaselectdtaselect-filter-files

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 19, 2018Dec 19, 2018

• MzIdentMLParser

  Public
  parser of mzIdentML files to read the data using the proteomics model from utilities artifact

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 19, 2018Dec 19, 2018

• TargetSeeker-MS

  Public
  TargetSeeker-MS is a Bayesian Inference approach for drug target discovery, using protein fractionation coupled to mass spectrometry. It identifies p…

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 1, 2018Oct 1, 2018

• RadialTopologyViewer

  Public
  RadialTopologyViewer performs a graphical visualization of a bait protein interactome derived from a co-immunoprecipitation experiment.

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 25, 2018Jul 25, 2018

• CoPIT

  Public
  Co-Purifying Protein Identification Technology (CoPIT) is a tool for the prediction of true interactors in single bait IP-MS

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 7, 2018Mar 7, 2018