Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster

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

(2014) Hao Wu et al.   BIOINFORMATICS

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

(2014) W. Huang et al.   GENOME RESEARCH

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

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Population- and Sex-Biased Gene Expression in the Excretion Organs of Drosophila melanogaster

(2014) Ann Kathrin Huylmans et al.   G3-Genes Genomes Genetics

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

(2013) Yuwen Liu et al.   BIOINFORMATICS

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

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

FlyBase 102—advanced approaches to interrogating FlyBase

(2013) Susan E. St. Pierre et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Franck Rapaport et al.   GENOME BIOLOGY

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

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

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay 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

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq

(2011) Lin Wang et al.   PLoS One

Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset

(2010) Qianqian Zhu et al.   BMC BIOINFORMATICS

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression in Aneuploid Drosophila S2 Cells

(2010) Yu Zhang et al.   PLOS BIOLOGY

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

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

The Sequence Alignment/Map format and SAMtools

(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

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

(2009) Joshua S Bloom et al.   BMC GENOMICS

Systems genetics of complex traits in Drosophila melanogaster

(2009) Julien F Ayroles et al.   NATURE GENETICS

Inferences and power analysis concerning two negative binomial distributions with an application to MRI lesion counts data

(2008) Inmaculada B. Aban et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH