EDyP laboratory projects

Welcome to the EDyP laboratory computation proteomics projects website, which contains the software projects developed and maintained by the EDyP members. Here is a list of software developed in our lab. For each of them you can find links to source code repository, documentation or downloads

Prostar

A R/Shiny application dedicated to the differential analysis of quantitative data resulting from discovery proteomics experiments
Prostar pages

Proline

A software environment for analysis of mass spectrometry based proteomics data to organize, collect, validate, quantify, visualize and publish proteomics datasets.
Proline pages

MzScope

Display and navigate MS data from mzdb files.
MzScope page

Mzdb converter / msData converter

Converts raw files from various mass spectrometer manufacturers into mzdb files.
mzdbConverter pages

MGFBoost

MGFBoost extract peaklists from raw MS data in mzdb format prior to search engine submission for peptide identification.
mgfBoost pages

ePims

A LIMS dedicated to mass spectrometry data.
ePims pages

Mascot Swissknife

A set of tools for fasta file and mascot databases
Mascot Swissknife pages

Proline Swissknife

A set of tools for simple proline data processing, accessing databases
Proline Swissknife pages

Histone PTM

A ‘R’ toolset to analyze histone PTMs proteomics data
Histone PTM pages

Well Plate Maker

The WPM allows users to generate well plate maps to carry out their experiments while improving the handling of batch effects
Well_Plate_Maker pages

ProteoRE

ProteoRE (Proteomics Research Environment) is a Galaxy-based platform for the functional analysis and the interpretation of proteomics and transcriptomics data in biomedical research
ProteoRE pages