Error estimates for the analysis of differential expression from RNA-seq count data

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments

(2013) Mikel Esnaola et al.   BMC BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

(2012) José A Robles et al.   BMC GENOMICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates

(2012) Steven P. Lund et al.   Statistical Applications in Genetics and Molecular Biology

Normalization, testing, and false discovery rate estimation for RNA-sequencing data

(2011) J. Li et al.   BIOSTATISTICS

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

(2011) Daniel Bottomly et al.   PLoS One

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS