vertesy / Seurat.Pipeline

Seurat Pipeline using the Seurat.utils package

Seurat Pipeline

Seurat Pipeline is an example single-cell analysis pipeline using Seurat and a set of custom packages developed for the Knoblich Lab.

Dependencies

Published Libraries Used

• Seurat
• tidyverse
• cowplot
• future
• doMC
• tictoc

Custom Function Libraries Used

• Seurat.utils
• Seurat.multicore (optional)
• CodeAndRoll
• ggExpressDev
• MarkdownReports

Install Function Libraries

# install.packages("devtools"); # If you don't have it.
require("devtools")

# Install dependencies
devtools::install_github(repo = "vertesy/Stringendo", upgrade = F)
devtools::install_github(repo = "vertesy/CodeAndRoll2", upgrade = F)
devtools::install_github(repo = "vertesy/ReadWriter", upgrade = F)
devtools::install_github(repo = "vertesy/MarkdownHelpers", upgrade = F)
devtools::install_github(repo = "vertesy/Markdownreports", upgrade = F)
devtools::install_github(repo = "vertesy/ggExpress", upgrade = F)
devtools::install_github(repo = "vertesy/Seurat.utils", upgrade = F)

# Install Seurat Pipeline

"Clone the repository"

Structure of the pipeline

There is one wrapper Frame script (“00.Frame.ProjectCode.etc.R”) in each projects. It loads Daughter scripts:

1. Custom scripts (All in the GitHub repo of the project, e.g. SEO) 2. Parameters script 2. Genelists scriptCustom Elements script

2. Reusable scripts (Seurat.pipeline repo)

   1. Elements scripts that are used in many projects

3. Custom Package

   1. MarkdownReports → See web for installation from Github.

4. Custom Function Libraries

   • Seurat.utils
   • Seurat.multicore (optional)
   • CodeAndRoll
   • ggExpressDev