Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size

TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks

(2017) Mohamed Zouine et al.   PLANT JOURNAL

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

(2016) Yanzhu Lin et al.   BMC GENOMICS

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

In Papyro Comparison of TMM (edgeR), RLE (DESeq2), and MRN Normalization Methods for a Simple Two-Conditions-Without-Replicates RNA-Seq Experimental Design

(2016) Elie Maza   Frontiers in Genetics

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment

(2015) Marek Gierliński et al.   BIOINFORMATICS

The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses

(2015) Kaifu Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

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

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

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis

(2015) Daniel Spies et al.   Computational and Structural Biotechnology Journal

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

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Hao Wu et al.   BIOINFORMATICS

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs

(2014) Mark A van de Wiel et al.   BMC BIOINFORMATICS

LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data

(2014) Bingqing Lin et al.   BMC GENOMICS

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

(2014) Zong Hong Zhang et al.   PLoS One

Power analysis and sample size estimation for RNA-Seq differential expression

(2014) Travers Ching et al.   RNA

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Error estimates for the analysis of differential expression from RNA-seq count data

(2014) Conrad J. Burden et al.   PeerJ

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

(2013) Ning Leng et al.   BIOINFORMATICS

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

(2013) Yuwen Liu et al.   BIOINFORMATICS

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression

(2013) Michele A. Busby et al.   BIOINFORMATICS

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

(2013) Danni Yu 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

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data

(2013) Yingtao Bi et al.   BMC 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

Calculating Sample Size Estimates for RNA Sequencing Data

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

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

(2012) Jianxing Feng et al.   BIOINFORMATICS

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors

(2012) M. A. Van De Wiel et al.   BIOSTATISTICS

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

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

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

(2012) H. Wu 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

CEDER: Accurate Detection of Differentially Expressed Genes by Combining Significance of Exons Using RNA-Seq

(2012) Lin Wan et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2012) Cole Trapnell et al.   Nature Protocols

Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates

(2012) Steven P. Lund et al.   Statistical Applications in Genetics and Molecular Biology

A powerful and flexible approach to the analysis of RNA sequence count data

(2011) Yi-Hui Zhou et al.   BIOINFORMATICS

Normalization, testing, and false discovery rate estimation for RNA-sequencing data

(2011) J. Li et al.   BIOSTATISTICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

(2011) Jason S. Cumbie et al.   PLoS One

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

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

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

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young 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

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

(2009) Likun Wang et al.   BIOINFORMATICS

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

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Regulatory Features Underlying Pollination-Dependent and -Independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling

(2009) H. Wang et al.   PLANT CELL

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