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.
- 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
- 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
- One-sample moderated T-test
- Two-sample moderated T-test
- Moderated F-test
- Heatmaps and cluster analysis
- Volcano plots
- Scatterplots
- Principle component analysis
- QC-plots
- Pairs-plots
- Correlation matrix
- Distribution of expression values
- Missing values
- Automatic converison of protein accession numbers (UniProt, RefSeq) to gene symbols
- Integration of protein-protein interaction databases (human only)
- InWeb
- BioGRID
- Reactome
- Results comprise high-quality figures (pdf), Excel-sheets and the R-workspace itself.
- All results can be downloaded as single zip-file.
- 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.