Siny/R app which provides a graphical interface for exploratory data analysis of single cell RNA-Seq data using R tools such as Bioconductor, Scater, Scran, EdgeR, Interactive Complex Heatamps & DataTables.

EdgeR interactive Complex Heatmaps Bioconductor Scran Scater DataTables for R

After installing any required packages from cran or bioconductor, start the app download or clone the ui.R and server.R files and open them with RStudio the click the run app button.

The app can also be hosted on a server and allowing user to run it through a browser based client. (Free servers on shinyapps.io have instufficent memory however)

Upload the three files from the cell ranger director (Matrix file, genes file, barcodes file) and a gene annotations file for the organsism.

After uploading the file inspecting the library size distributions should show if there was a major problem in the data.

The next stage we filter the data. Removing duplicated and unAnnotated genes is necessary for following data analysis. Removing genes where only a small percentage of cells have non-zero counts is recommended. Adjusting the minimum percentage should yield an appropriate distribution of counts.

The next step is to normailze counts with respect each cells library size. Since we expect biological as well as techinical differences in library size we first perform a basic clustering of cells of similar expression profiles and only normalize with respect to cells in the same cluster.

Scran computes the technical and biological variance of each gene. Using the table or the graph we can select the genes we wish to include in further analysis.

Plot the exprssion of the genes by selecting them from the table.