PfizerRD / protigy

Proteomics Toolset for Integrative Data Analysis

This Shiny app facilitates exploratory and interactive analysis of data sets derived from quantitative proteomics experiments, RNA-seq and gene expression microarrays.

The app can run locally on your Desktop computer (Windows/Linux/MAC) or can deployed to Shiny Server environments. To access all implemented features the app has to run on a Shiny Server Pro (SSP) instance, see below for a summary of features only available in SSP.

Supported input formats:

• Any type of text file containing both, expression and annotation columns, can directly be imported into the app.
• Supported file formats:
  • text files (tsv, csv, txt)
  • gct 1.2
  • NEW gct 1.3

Data manipulation:

• Transformation
  • log transformation
• Sample-wise Normalization
  • Centering (median)
  • Centering and scaling (median-MAD)
  • Quantile
  • 2-component
• Filtering
  • Reproducibility filter across replicate measurements
  • Standard deviation across samples

Marker selection (based on limma package)

• One-sample moderated T-test
• Two-sample moderated T-test
• Moderated F-test

Interactive data analysis and visualization

• Heatmaps and cluster analysis
• Volcano plots
• Scatterplots
• Principle component analysis
• QC-plots
  • Pairs-plots
  • Correlation matrix
  • Distribution of expression values
  • Missing values

Proteomics-specific features

• Automatic converison of protein accession numbers (UniProt, RefSeq) to gene symbols
• Integration of protein-protein interaction databases (human only)
  • InWeb
  • BioGRID
  • Reactome

Export of analysis results

• Results comprise high-quality figures (pdf), Excel-sheets and the R-workspace itself.
• All results can be downloaded as single zip-file.

Shiny Server Pro specific features

• User authentification as provided by SSP.
• Save and retrieve app-sessions on the server.

This app is being developed and maintained at the Proteomics Platform of the Broad Institute of MIT and Harvard.

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