Discover Prostar

Prostar is a software tool dedicated to the differential analysis of quantitative data resulting from discovery proteomics experiments.

Prostar is easy to install (see our Zero-install page), easy to use (thanks to its Shiny-based click-button interface) and well-documented (see our reference page). Moreover, it has been regularly updated along years to provide state-of-the-art data science methodologies.

Presentation

Data management

  • Conversion: To import a tabulated file containing quantitative data and convert it into an MSnset structure.
  • Loading: To open an Msnset structure that has been previously constructed.
  • Exporting: To save a partially/completely processed dataset and to download the data analysis results.
  • Demo data: Toy datasets are available to discover Prostar potential in the simplest way.

Data processing

  • Filtering: To prune the protein or peptide list according to various criteria (missing values, string matching).
  • Normalization: To correct batch or group effects.
  • **Imputation: By taking into account the very nature of each missing value.
  • Aggregation: For peptide-level datasets, it is possible to estimate protein abundances.
  • Hypothesis testing: To compute the significance of each protein differential abundance.

Data mining

  • Descriptive statistics: Available at any stage of the analysis, for data exploration and visualization.
  • Peptide-Protein Graph: Explore and visualize peptide-protein graphs.
  • Differential analysis: To select a list of differentially abundant proteins with a controlled false discovery rate.
  • Gene Ontology analysis: To map a protein list onto GO terms and test category enrichment.

Software

  1. Zero-install
    The easiest way. Prostar is deployed either as a zip archive (so far only available on Microsoft Windows desktop machines) or as a Docker image (bêta, but ok for Windows, Mac OS X and (Unix/Linux).
  2. Stand-alone Bioconductor install
    The standard method to install Bioconductor distributed software. This method works for any operating systems (Unix/Linux, Mac OS X and Windows) as long as R is installed.
  3. Server install
    When one wants Prostar to run on a Unix server, on which remote users connect. This more advanced type of install is detailed in the user manual.
  4. Online demo
    Before installing Prostar on your desktop machine, test our online demo!