consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction

Stability of methods for differential expression analysis of RNA-seq data

(2019) Bingqing Lin et al.   BMC GENOMICS

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis

(2019) Verónica Jiménez-Jacinto et al.   Frontiers in Genetics

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

(2017) Juliana Costa-Silva et al.   PLoS One

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data

(2016) Hugo Varet et al.   PLoS One

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns

(2014) Panagiotis Moulos et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells

(2014) Blanca E. Himes et al.   PLoS One

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

(2014) Yan Guo et al.   Biomed Research International

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

easyRNASeq: a bioconductor package for processing RNA-Seq data

(2012) N. Delhomme et al.   BIOINFORMATICS

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

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

(2011) Daniel Bottomly et al.   PLoS One

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

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