The main materials are included in the SingleCellWorkFlow.Rmd file. Set the working directory in RStudio to the folder containing this file, open the file and click Knit on the toolbar of the editor. This generates the full report with the relevant plots.

Download this workflow either using git to create the "ABACBS2017Workshop" folder:

git clone https://github.com/Shians/ABACBS2017Workshop.git

or click "Clone or Download" > "Download Zip" on the top right of the panel followed by unzipping the data into the desired directory.

This cam be done in R

utils::download.file("https://github.com/Shians/ABACBS2017Workshop/archive/master.zip", destfile = "master.zip")
utils::unzip("master.zip")

The packages used in this workflow can be installed by the following code

source("https://bioconductor.org/biocLite.R")
biocLite(c("scPipe", "scater", "scran", "SC3", "edgeR", "Glimma"), suppressUpdates=TRUE)
install.packages(c("dplyr", "stringr", "magrittr", "ggplot2", "tibble", "plotly", "Rtsne"))

for those on the BioC Amazon instance, only the Rtsne package needs to be added

install.packages("Rtsne")

This workflow is adapted from other vignettes and workflows.

• scPipe
• scater
• A step-by-step workflow for low-level analysis of single-cell RNA-seq data
• RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Please help me develop this workflow by asking questions about any confusing statements or code. Leave an issue on this Github repository or email me.