User profiles for Gordon K. Smyth
 | Gordon K SmythDivision Head, Bioinformatics, Walter and Eliza Hall Institute of Medical Research Verified email at wehi.edu.au Cited by 192909 |
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
It is expected that emerging digital gene expression (DGE) technologies will overtake
microarray technologies in the near future for many functional genomics applications. One of the …
microarray technologies in the near future for many functional genomics applications. One of the …
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
GK Smyth - Statistical applications in genetics and molecular …, 2004 - degruyter.com
The problem of identifying differentially expressed genes in designed microarray experiments
is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds …
is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds …
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Motivation: Next-generation sequencing technologies generate millions of short sequence
reads, which are usually aligned to a reference genome. In many applications, the key …
reads, which are usually aligned to a reference genome. In many applications, the key …
[HTML][HTML] limma powers differential expression analyses for RNA-sequencing and microarray studies
limma is an R/Bioconductor software package that provides an integrated solution for analysing
data from gene expression experiments. It contains rich features for handling complex …
data from gene expression experiments. It contains rich features for handling complex …
Limma: linear models for microarray data
GK Smyth - … and computational biology solutions using R and …, 2005 - Springer
A survey is given of differential expression analyses using the linear modeling features of
the limma package. The chapter starts with the simplest replicated designs and progresses …
the limma package. The chapter starts with the simplest replicated designs and progresses …
[HTML][HTML] voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq
experiments. The voom method estimates the mean-variance relationship of the log-…
experiments. The voom method estimates the mean-variance relationship of the log-…
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
A flexible statistical framework is developed for the analysis of read counts from RNA-Seq
gene expression studies. It provides the ability to analyse complex experiments involving …
gene expression studies. It provides the ability to analyse complex experiments involving …
[HTML][HTML] Gene ontology analysis for RNA-seq: accounting for selection bias
We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq
data. GO analysis is widely used to reduce complexity and highlight biological processes in …
data. GO analysis is widely used to reduce complexity and highlight biological processes in …
Orchestrating high-throughput genomic analysis with Bioconductor
Bioconductor is an open-source, open-development software project for the analysis and
comprehension of high-throughput data in genomics and molecular biology. The project aims …
comprehension of high-throughput data in genomics and molecular biology. The project aims …
Generation of a functional mammary gland from a single stem cell
…, F Vaillant, KJ Simpson, J Stingl, GK Smyth… - Nature, 2006 - nature.com
The existence of mammary stem cells (MaSCs) has been postulated from evidence that the
mammary gland can be regenerated by transplantation of epithelial fragments in mice 1 , 2 , …
mammary gland can be regenerated by transplantation of epithelial fragments in mice 1 , 2 , …