---
title: A brief introduction to edgeR
date: "10 October 2012 (last revised 21 June 2023)"
output:
  BiocStyle::html_document:
    toc: FALSE
    number_sections: FALSE
vignette: >
  %\VignetteIndexEntry{A brief introduction to edgeR}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  prompt = TRUE,
  comment = NA
)
```

# What is it?

edgeR is a package for differential analyses of read count data from sequencing technologies
such as RNA-seq, ChIP-seq, ATAC-seq, BS-seq and CUT&RUN.
It has particularly strong capabilities for expression analyses of RNA-seq data, including gene expression, transcript expression and tests for differential splicing.

edgeR implements novel statistical methods based on the negative binomial distribution
as a model for count variability, including empirical Bayes methods, exact tests, and generalized linear models.
The package is especially suitable for analysing designed experiments with multiple
experimental factors but possibly small numbers of replicates.
It has unique abilities to model transcript specific variation even in small samples,
a capability essential for prioritizing genes or transcripts that have consistent effects across replicates.

# How to get help

The edgeR User's Guide is available by
```{r, eval=FALSE, echo=TRUE}
library(edgeR)
edgeRUsersGuide()
```
or alternatively from the [edgeR landing page](https://bioconductor.org/packages/edgeR).

Documentation for specific functions is available through the usual R help system, e.g., `?glmFit`.
Further questions about the package should be directed to the [Bioconductor support site](https://support.bioconductor.org).

# Further reading

Chen Y, Chen L, Lun ATL, Baldoni PL, Smyth GK (2024). edgeR 4.0: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. *bioRxiv* doi: [10.1101/2024.01.21.576131](https://doi.org/10.1101/2024.01.21.576131).

Chen, Y, Pal, B, Visvader, JE, Smyth, GK (2017). Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. *F1000Research* 6, 2055. [doi:10.12688/f1000research.13196.2](https://doi.org/10.12688/f1000research.13196.2)

Chen Y, Lun ATL, Smyth GK (2016). From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. *F1000Research* 5, 1438. [doi:10.12688/f1000research.8987.2](https://doi.org/10.12688/f1000research.8987.2)

McCarthy, DJ, Chen, Y, Smyth, GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. *Nucleic Acids Research* 40, 4288-4297. [doi:10.1093/nar/gks042](https://doi.org/10.1093/nar/gks042)

Robinson, MD, McCarthy, DJ, Smyth, GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. *Bioinformatics* 26, 139-140. [doi:10.1093/bioinformatics/btp616](https://doi.org/10.1093/bioinformatics/btp616)