Getting Started with scPipeline

Setup

R version 4.0 or greater is required. We also recommend installing R Studio.

scPipeline is available as a series of RMarkdown stripts and the latest version of scPipeline source code can be found on scPipeline github repository. To setup and run scPipeline, download the repository locally:

Option 1: Clone git repository with Bash

git clone https://github.com/NMikolajewicz/scPipeline
cd scPipeline

Option 2: Clone git repository with RStudio

In RStudio, navigate to file -> New Project... -> Version Control -> Git. You will then be prompted to provide the git repository information:

Repository URL: https://github.com/NMikolajewicz/scPipeline
Project Directory Name: scPipeline

Press Create Project and you’re good to go!

Required Packages

scPipeline is dependent on our scMiko package. Please find installation instructions here prior to proceeding with scPipeline.

scPipeline is also dependent on flexdashboards to generate interactive dashboards using R Markdown. The flexdashboard package can be installed from CRAN as follows:

install.packages("flexdashboard")

Additionally, each scPipeline module depends on a variety of R packages to run, and a complete list of required packages can be found at the beginning of each module script.

To install multiple R packages simultaneously, the following command can be used:

# example
install.packages(c("Seurat", "presto", "dplyr", "tidyr", "stringr", "RColorBrewer", "ggplot2", "DT",
    "flexdashboard", "ggrepel", "future", "ggwordcloud", "scales", "org.Mm.eg.db", "org.Hs.eg.db",
    "parallel", "doParallel", "foreach"))

Running scPipeline Modules

Running scPipeline modules is like running any other Rmarkdown script:

Open a scPipeline module script (.Rmd) in RStudio.
Specify analysis parameters
- See Module Overviews for instructions.
Run scPipeline Module. Each scPipeline module can be run in one of two ways:
1. knit document (recommended)
  - Renders an .HTML report
2. Run chunk-by-chunk
  - If print.inline = TRUE, figures are printing within the R markdown file.
  - Does not render an .HTML report.
  - This option permit users to customize their analyses beyond what has been provided by us.

Please refer to these tutorial slides for additional step-by-step instructions on how to get scPipeline running.

scPipeline .HTML reports

Every scPipeline Module generates an HTML report summarizing the analysis results. These can be viewed using any browser. Given their portability (i.e., self-contained), these can be shared easily shared among users. HTML reports are generated using flexdashboard.