🎯 Welcome to CAIBIrnaseq

CAIBIrnaseq is an R package designed to streamline, standardize, and reproduce key steps of gene expression analysis from RNA-seq data. Developed by the CAIBI platform team, it integrates powerful tools for:

• Preprocessing raw expression data (TPM calculation, filtering, normalization, etc.)
• Exploratory data analysis (PCA, clustering, heatmaps)
• Differential expression analysis (DESeq2 and visualization of DE genes)
• Functional and pathway analysis (FGSEA, ORA, PROGENy scoring)
• Tumor microenvironment investigation (MCPcounter, cell-type signatures)

Quick Installation

In RStudio, try running these command lines :

# If not already installed
install.packages("devtools")
install.packages("BiocManager")

# Installation from Github :
devtools::install_github("crcordeliers/CAIBIrnaseq", dependencies = TRUE)

If you have any problems, more informations about installation are available on our package website : https://crcordeliers.github.io/CAIBIrnaseq/

We hope this will help you in your projects !!!