Hi there,

Would anyone know the correct way to create a citation for edgeR user manual ? I wasn't sure whether to cite the original edgeR paper or if the user manual needs a separate citation?

Thanks

Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The User's Guide isn't recognized as a formal academic publication so we don't get any academic credit when you cite it. We prefer that you cite the journal papers.

Section 1.2 of the User's Guide advises how to cite the different edgeR pipelines. If you type citation("edgeR") at the R prompt, it suggests the following four papers:

• Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140

• McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 40, 4288-4297

• 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

• 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 https://doi.org/10.1101/2024.01.21.576131.

Going forward, the new edgeR 4.0 reference (the last paper listed) would be the best. Yunshun Chen, who is first author of that paper, has been the lead maintainer of edgeR for over a decade.