Document

We provide the R script needed to reproduce the processed scRNA-seq datasets results of PlantPhoneDB.

Quick Installation

First, install devtools (for installing GitHub packages) if it isn’t already installed:

if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")

Then, install BiocManager (for installing bioconductor packages) if it isn’t already installed:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

Also, install from CRAN:

install.packages('Seurat')
library(Seurat)

Then, install sceasy, data.table, readxl and anndata, etc. Once all the dependencies are downloaded and loaded, you can run this R script below for analyzing scRNA-seq datasets collected by PlantPhoneDB.

using_example.ipynb was used for analyzing scRNA-seq datasets collected by PlantPhoneDB.

---

We provide the R script needed to reproduce analyze results of Case 1 (Figure 5), significant cell-cell interactions of Heat-Shocked Root Cells in Arabidopsis thaliana.

Case1.ipynb was used to infer cell-cell communications from scRNA-seq datasets processed by using_example.ipynb.