As you may have noticed from the update history, this hasn't received much attention from me recently. If you're interested in applying the workflow or visualization tool to your data, please get in touch with me (www.baderlab.org/BrendanInnes).
A pipeline and data visualization tool for Dropseq data
pipeline.Rmd for the R notebook that can be run in RStudio.
pipeline.md for an example of the pipeline report.
pipeline.md.html for the html version of the report, the default output of the R notebook.
pipelineViz.R for the R script containing the Shiny app.