RNAseq analysis with DEseq2 and functional enrichment analysis

Interested in exploring more applications of the RNASeq, Please read here more https://doi.org/10.1093/bib/bbab259

About the RNA-Seq analysis

The R script performs several steps in RNAseq gene differential expression analysis, including filtering, preprocessing, visualization, clustering, and Enrichment. For the analysis, several R Bioconductor packages are required to be installed (Installation commands are provided in the script. However, users can also refer to the Bioconductor website for detailed instructions).

Required data files

You should have a raw count and annotation/metadata file for running this analysis. Raw count files are usually obtained from tools such as featureCount, Rsem etc.

Bioconductor packages to be installed

DESeq2

edgeR

biomaRt (Very useful for gene filtering and annotations)

PCAtools (PCA detailed analysis)

ReactomePA (enrichment analysis)