RNA-Seq differential expression analysis: An extended review and a software tool

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

(2017) Sayed Mohammad Ebrahim Sahraeian et al.   Nature Communications

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

(2016) Nicholas J. Schurch et al.   RNA

Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

(2015) Peipei Li et al.   BMC BIOINFORMATICS

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

(2015) Sonia Tarazona et al.   NUCLEIC ACIDS RESEARCH

The devil in the details of RNA-seq

(2014) Anton Kratz et al.   NATURE BIOTECHNOLOGY

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data

(2014) Zong Hong Zhang et al.   PLoS One

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

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

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Comparison of software packages for detecting differential expression in RNA-seq studies

(2013) F. Seyednasrollah et al.   BRIEFINGS IN BIOINFORMATICS

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Assessing the gain of biological data integration in gene networks inference

(2012) Fábio FR Vicente et al.   BMC GENOMICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

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

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

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

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

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

(2010) Ashish Agarwal et al.   BMC GENOMICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

bioDBnet: the biological database network

(2009) Uma Mudunuri et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

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

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

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

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