PROPER: comprehensive power evaluation for differential expression using RNA-seq

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data

(2013) Chung-I Li et al.   BMC BIOINFORMATICS

Calculating Sample Size Estimates for RNA Sequencing Data

(2013) Steven N. Hart et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data

(2012) H. Wu et al.   BIOSTATISTICS

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

(2011) Alyssa C Frazee et al.   BMC BIOINFORMATICS

Design and validation issues in RNA-seq experiments

(2011) Z. Fang et al.   BRIEFINGS IN BIOINFORMATICS

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

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

(2011) Daniel Bottomly et al.   PLoS One

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

(2010) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

Polymorphic Cis- and Trans-Regulation of Human Gene Expression

(2010) Vivian G. Cheung et al.   PLOS 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

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS