Assessing Dissimilarity Measures for Sample-Based Hierarchical Clustering of RNA Sequencing Data Using Plasmode Datasets

Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models

(2015) Andrea Rau et al.   BIOINFORMATICS

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

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Model-based clustering for RNA-seq data

(2013) Yaqing Si et al.   BIOINFORMATICS

Data-based filtering for replicated high-throughput transcriptome sequencing experiments

(2013) Andrea Rau et al.   BIOINFORMATICS

Accounting for noise when clustering biological data

(2012) R. Sloutsky et al.   BRIEFINGS IN BIOINFORMATICS

Application of the Gini Correlation Coefficient to Infer Regulatory Relationships in Transcriptome Analysis

(2012) C. Ma et al.   PLANT PHYSIOLOGY

Classification and clustering of sequencing data using a Poisson model

(2011) Daniela M. Witten   Annals of Applied Statistics

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

(2011) Alyssa C Frazee et al.   BMC BIOINFORMATICS

Genome-Wide Linkage Analysis of Global Gene Expression in Loin Muscle Tissue Identifies Candidate Genes in Pigs

(2011) Juan Pedro Steibel et al.   PLoS One

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

(2011) Daniel Bottomly et al.   PLoS One

Filtering, FDR and power

(2010) Maarten van Iterson 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

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

(2010) Andrew J Severin et al.   BMC PLANT BIOLOGY

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

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

Clustering Algorithms: On Learning, Validation, Performance, and Applications to Genomics

(2009) Lori Dalton et al.   CURRENT GENOMICS

The use of plasmodes as a supplement to simulations: A simple example evaluating individual admixture estimation methodologies

(2008) Laura K. Vaughan 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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Evaluating Statistical Methods Using Plasmode Data Sets in the Age of Massive Public Databases: An Illustration Using False Discovery Rates

(2008) Gary L. Gadbury et al.   PLoS Genetics