Baldoni PL, Chen L, Smyth GK. Faster and more accurate assessment of differential transcript expression with Gibbs sampling and edgeR v4. NAR Genomics and Bioinformatics. 2024;6(4):10.1093/nargab/lqae151
Baldoni PL, Chen Y, Hediyeh-zadeh S, Liao Y, Dong X, Ritchie ME, Shi W, Smyth GK. Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR. Nucleic Acids Research. 2024;52(3):10.1093/nar/gkad1167
Li M, Smyth GK. Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics. Bioinformatics. 2023;39(5):10.1093/bioinformatics/btad200
Chen Y, Pal B, Lindeman GJ, Visvader JE, Smyth GK. R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue. Scientific Data. 2022;9(1):10.1038/s41597-022-01236-2
Liao Y, Smyth GK, Shi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Research. 2019;47(8):10.1093/nar/gkz114
Chen Y, Pal B, Visvader JE, Smyth GK. Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. F1000Research. 2017;6:10.12688/f1000research.13196.1
Chen Y, Pal B, Visvader JE, Smyth GK. Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. F1000Research. 2017;6:10.12688/f1000research.13196.2
Chen Y, Lun ATL, Smyth GK. From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research. 2016;5:10.12688/f1000research.8987.1
Phipson B, Lee S, Majewski IJ, Alexander WS, Smyth GK. Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression. The Annals of Applied Statistics. 2016;10(2):10.1214/16-aoas920
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research. 2015;43(7):10.1093/nar/gkv007
