Setting up

Install R

R can be installed from the R-project website.

Direct downloads for all platforms can be downloaded at the links below:

Mac

Windows

Linux

Install RStudio

RStudio can be installed from the RStudio website.

RStudio can be downloaded for all platforms at the link below:

https://rstudio.com/products/rstudio/download/

Install required packages

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("edgeR")
BiocManager::install("GenomicAlignments")
BiocManager::install("Rsubread")
BiocManager::install("Biostrings")
BiocManager::install("AnnotationDbi")
BiocManager::install("org.Hs.eg.db")
install.packages("ggplot2")
install.packages("DT")
install.packages("ggrepel")
install.packages("RColorBrewer")
BiocManager::install("Glimma")
BiocManager::install("GO.db")

Load required packages

library(edgeR)
library(GenomicAlignments)
library(Rsubread)
library(Biostrings)
library(AnnotationDbi)
library(org.Hs.eg.db)
library(ggplot2)
library(DT)
library(ggrepel)
library(RColorBrewer)
library(Glimma)
library(GO.db)

Download the material

The sequencing files and human GeCKO sgRNA library can be downloaded from the github repository by clicking on the following links.

Create necessary directories

dir.create("./index")
dir.create("./RData")
dir.create("./tables")
dir.create("./figures")