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 allows researchers to apply a large range of bioinformatics tools and tailored workflows on their own data using Galaxy capabilities. ProteoRE comprises 21 tools organized into four subsections: i) data manipulation and visualization; ii) get features/annotation; iii ) functional analysis; and iv) pathway analysis along with graphical representation. This version also includes Galaxy generic tools and some tools from the GalaxyP project that should be of great help for (re)processing MS-based proteomics data (e.g. peptide/protein identification).
ProteoRE new release (24th June 2024) - release notes
ProteoRE server: CPU and memory resources have been extended and jobs management configuration revisited to better satisfy user needs
This public site is meant for academic usage; for commercial usage, contact us). ProteoRE can currently be used as:
Unregistered user: you can analyze your data (e.g. proteomics identification results in tab format) using the available tools. Allocated storage space is limited to 20 Mb and data/history/analyses are not conserved between sessions.
Registered user (password-protected access): we recommend to create a user account. Up to 20 Gb storage space is offered to registered users, along with access to shared resources (data, histories, workflows..). To create an account: click on "Account registration or login" on the main menu bar (upper part of the ProteoRE central panel), click on "registration" and fill out the form. Once the form is submitted, your account is created.
ProteoRE Tutorials available in Galaxy Training Network:
If you use resources from ProteoRE, please cite: Mehta S, et al. A Galaxy of informatics resources for MS-based proteomics. Expert Rev Proteomics. 2023, 20(11):251-266. doi: 10.1080/14789450.2023.2265062. PMID: 37787106.
How to contribute?
As a developper/bioinformatician: ProteoRE team welcomes any contribution via GitHub, please read here
As a biologist/clinician: ProteoRE is constantly evolving and we greatly appreciate users feedbacks helping at improving ProteoRE capabilities: contact us !
Welcome to ProteoRE !