Single Cell RNA-Seq analysis with Seurat

Waldeyr Mendes Cordeiro da Silva; compiled on Apr-2021

This R notebook is the code used in a case study of the Chapter "Transcriptome Analysis Throughout RNA-seq" by Silva et al.

The basic environment is a Linux with R version 4.x. I recomend to setup the environment and run it using anaconda by following the steps:

Download and install anaconda anaconda
Create a conda environment with R version > 4 conda create --name r4-base
Activate the r4-base environment to use it conda activate r4-base
Install R v4.x and the jupyter notebook conda install -c conda-forge r-base jupyter git
Open the R console and install/configure

install.packages('IRkernel')

IRkernel::installspec()

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.12")

BiocManager::install('ggplot2')

BiocManager::install('ggrepel')

BiocManager::install('limma')

BiocManager::install('calibrate')

BiocManager::install('dplyr')

BiocManager::install('Matrix')

BiocManager::install('Seurat') # It requires R version 4.x

quit()

git clone https://github.com/waldeyr/single_cell_analysis.git

jupyter-notebook