MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality Control

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

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Evaluation of read count based RNAseq analysis methods

(2013) Yan Guo et al.   BMC GENOMICS

Three-stage quality control strategies for DNA re-sequencing data

(2013) Y. Guo et al.   BRIEFINGS IN BIOINFORMATICS

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data

(2013) Yan Guo et al.   PLoS One

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq

(2011) Yanming Di et al.   Statistical Applications in Genetics and Molecular Biology

A Two-Stage Poisson Model for Testing RNA-Seq Data

(2011) Paul L. Auer et al.   Statistical Applications in Genetics and Molecular Biology

Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data

(2011) Jun Li et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

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

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

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

(2009) Yan W Asmann et al.   BMC GENOMICS

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

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

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

The beginning of the end for microarrays?

(2008) Jay Shendure   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS