Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq
The code for the paper Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq. The data is available here. First, you should clone the repo:
git clone https://github.com/Bastien-mva/pipeline_seurat_monocle.git
cd pipeline_seurat_monocle
You should put the downloaded data inside this respository. Then unzip it. To run the script, you must install the following packages:
- dplyr
- Seurat
- ggplot2
- patchwork
- ggpubr
- monocle3
- SeuratWrappers
- ff
You can then run
Rscript pipeline.R
Alternatively you can run it in Rstudio.
Many of the available plots in the paper are taken
from this script, and all the plots coming from Seurat and Monocle can be
derived changing only arguments in the pipeline.R script (for example changing
the name of genes for UMAP plots). Note that the script choose the root node
for pseudotime analysis automatically, so that the script can be run from the command line.
Comments indicate how to choose the root node manually if you are in
interactive mode (for example Rstudio).
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