Seurat Pipeline is an example single-cell analysis pipeline using Seurat and a set of custom packages developed for the Knoblich Lab.
- Seurat
- tidyverse
- cowplot
- future
- doMC
- tictoc
# 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"
There is one wrapper Frame script (“00.Frame.ProjectCode.etc.R”) in each projects. It loads Daughter scripts:
-
Custom scripts (All in the GitHub repo of the project, e.g. SEO) 2. Parameters script 2. Genelists scriptCustom Elements script
-
Reusable scripts (Seurat.pipeline repo)
- Elements scripts that are used in many projects
-
Custom Package
- MarkdownReports → See web for installation from Github.
-
Custom Function Libraries
- Seurat.utils
- Seurat.multicore (optional)
- CodeAndRoll
- ggExpressDev