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 as a zip archive (so far only available on Microsoft Windows desktop machines).
  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.