Workflow for low-level scRNA-seq data analyses

To run this workflow:

1. Run add_figure.sh to generate dynamic figure numbers.
2. Download the files containing the count data for each study from public repositories. (This can be done by running the code block containing all.urls <- from raw_workflow.Rmd. Alternatively, set on.bioc <- TRUE in workflow.Rmd, though this will also delete the files at the end of the workflow.)
3. Run knitr::knit("workflow.Rmd") in R to compile the workflow.
4. Run rmarkdown::render("workflow.md") in R to generate a HTML report.