Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them)

(2011) D. Berrar et al.   BRIEFINGS IN BIOINFORMATICS

Transposase mediated construction of RNA-seq libraries

(2011) J. Gertz et al.   GENOME RESEARCH

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Hybridization thermodynamics of NimbleGen Microarrays

(2010) Ulrike Mueckstein et al.   BMC BIOINFORMATICS

G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration

(2010) Mario Fasold et al.   BMC BIOINFORMATICS

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell 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

Consolidated strategy for the analysis of microarray spike-in data

(2008) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed-tissue RNA reference samples

(2008) PS Pine et al.   PHARMACOGENOMICS