Single Cell Transcriptomics

Introduction

• Install R package for single cell transcriptome analysis using Conda.
• Install Seurat (suh-RAHT) R package

Create R environment and install Seurat using Conda

Create an environment for R based single cell transcriptomics analysis (Seurat)

Install R

conda create -n scrna_r_env r-base=4.3 -y
conda activate scrna_r_env 

Install Seurat package

conda activate scrna_r_env
conda install -c conda-forge r-irkernel r-seurat

Register interactive R kernel

Execute the following command in R to register interactive R kernel.

IRkernel::installspec()

Use JupyterNotebook to execute R

• Connect to the BDSL server using remote SSH in Visual Studio Code.
• Create a JupyterNotebook
• Choose R Kernel
  • Similar to ~/anaconda3/envs/scrna_r_env/lib/R/bin/R
• Use R script