Repositories list

• RawConverter

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

  C#

  •

  Apache License 2.0

  •1•1•0•0•Updated Aug 8, 2024Aug 8, 2024

• PINT

  Public
  PINT is a new comprehensive web-based system to store, visualize, and query experimental proteomics data obtained under different experimental conditions and projects. PINT provides a very powerful query system through the use of different proteomics-specific data query commands running over both the experimental features and external annotation…

  pythondatabaseproteins+ 11annotationsdata-integrationuniprotprotein-quantificationwikipintexperimental-conditions+ 4

  Java

  •

  Apache License 2.0

  •0•4•1•6•Updated Aug 6, 2024Aug 6, 2024

• utilities

  Public
  General Java util classes used across different projects

  data-modelutility-libraryproteomics+ 1proteomics-data

  Java

  •

  Apache License 2.0

  •1•0•0•4•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-to-protein relationship and to visualize the results in a bipartite network (Cytoscape).

  javaproteincytoscape+ 17proteomicsproteomics-datalabel-free-quantificationredundancysalvadorquantitative-analysisquantitation+ 10

  Python

  •3•6•0•0•Updated Aug 23, 2023Aug 23, 2023

• proteoform_dbIndex

  Public
  extension of dbIndex module to index proteoforms

  Java

  •

  Apache License 2.0

  •1•0•0•0•Updated Aug 23, 2023Aug 23, 2023

• QuantParser

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

  proteomicsproteomics-datalabel-free-quantification+ 7isotopologueisobaric-quantificationsanxotparserparsecensusquantitative-data

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 16, 2023Jun 16, 2023

• dbIndex

  Public
  Indexing of FASTA files for searching peptide masses and sequences

  databaseindexingfasta+ 3proteomicsproteomics-dataproteomics-datasets

  Java

  •

  Apache License 2.0

  •0•0•0•1•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 specific sites in the structure of the protein

  Java

  •

  Apache License 2.0

  •0•0•0•1•Updated Apr 17, 2023Apr 17, 2023

• mokapot

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

  Python

  •

  Apache License 2.0

  •16•0•0•0•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 data from IP2 (quant compare output files) and MaxQuant.

  proteomicsglycoproteomicsglycosylation+ 1glycomsquant

  Java

  •

  Apache License 2.0

  •0•2•1•0•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 proteins with certain relative expression values. This process is done by using a database of datasets of RNASeq expression values from single cells from which the cell type is known (or…

  javarna-seqstatistics+ 10rshinycellproteomicssingle-cellenrichment-analysiskolmogorov-smirnovcelltype+ 3

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 5, 2022Jan 5, 2022

• DTASelectParser

  Public
  Java parser for DTASelect output files

  parserparser-libraryproteomics+ 2dtaselectjavaparser

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Aug 11, 2021Aug 11, 2021

• CensusTMT2MSstatsTMT

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

  converterproteomicsproteomics-data+ 3censusmsstatstmt

  Java

  •

  Apache License 2.0

  •1•0•0•0•Updated Aug 2, 2021Aug 2, 2021

• ViSEAGO_Shiny

  Public
  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Jul 30, 2021Jul 30, 2021

• pcomplex

  Public
  Java

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  Apache License 2.0

  •0•0•0•0•Updated Jul 27, 2021Jul 27, 2021

• 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 transfer them to an external FTP site, such as MassIVE

  transferdtaselect-filesssh-credentials

  Java

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  Apache License 2.0

  •0•0•0•0•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

  •0•0•2•0•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

  hupo-psiconverterformat-converter+ 3mzidentmldtaselectdtaselect-filter-files

  Java

  •

  Apache License 2.0

  •0•0•1•0•Updated Jul 20, 2020Jul 20, 2020

• Dilu

  Public
  C

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 8, 2019Oct 8, 2019

• PCQ_GUI

  Public
  Apache License 2.0

  •0•0•0•0•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

  •0•0•0•0•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)

  rtdtaselect-filter-filesretention-time+ 2dtaselectms2

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Apr 17, 2019Apr 17, 2019

• DTASelect2PepXML

  Public
  Converter from DTASelect to pepXML formats

  proteomicsproteomics-datadata-conversion+ 7dtaselectdtaselect-filter-filesspectrumconvertertpppeptidespepxml

  Java

  •

  Apache License 2.0

  •0•0•0•0•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

  •0•0•0•0•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 proteins that are statistically significantly enriched via generating a noise-model using Bayesian Inference, which are measured with high reproducibility across a set of replicates.

  Java

  •0•0•0•0•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

  •0•0•0•0•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

  •0•0•0•0•Updated Mar 7, 2018Mar 7, 2018