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

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

(2014) S. Anders et al.   BIOINFORMATICS

Pax5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia

(2014) G. J. Liu et al.   GENES & DEVELOPMENT

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

(2014) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Charity W Law et al.   GENOME BIOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

Separate-channel analysis of two-channel microarrays: recovering inter-spot information

(2013) Gordon K Smyth et al.   BMC BIOINFORMATICS

Guide: a desktop application for analysing gene expression data

(2013) Jarny Choi   BMC GENOMICS

Gene-expression data integration to squamous cell lung cancer subtypes reveals drug sensitivity

(2013) D Wu et al.   BRITISH JOURNAL OF CANCER

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

(2013) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity

(2013) Adi L. Tarca et al.   PLoS One

The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease

(2013) D. Wu et al.   RNA

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

(2013) Franck Rapaport et al.   GENOME BIOLOGY

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

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

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts

(2011) Massimiliano Caiazzo et al.   NATURE

RPPanalyzer: Analysis of reverse-phase protein array data

(2010) Heiko A. Mannsperger et al.   BIOINFORMATICS

ROAST: rotation gene set tests for complex microarray experiments

(2010) Di Wu et al.   BIOINFORMATICS

Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells

(2010) I. J. Majewski et al.   BLOOD

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Control of mammary stem cell function by steroid hormone signalling

(2010) Marie-Liesse Asselin-Labat et al.   NATURE

Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips

(2010) Wei Shi et al.   NUCLEIC ACIDS RESEARCH

Estimating the proportion of microarray probes expressed in an RNA sample

(2010) Wei Shi et al.   NUCLEIC ACIDS RESEARCH

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

Testing significance relative to a fold-change threshold is a TREAT

(2009) D. J. McCarthy et al.   BIOINFORMATICS

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

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

Integrative analysis of RUNX1 downstream pathways and target genes

(2009) Joëlle Michaud et al.   BMC GENOMICS

Aire-Deficient C57BL/6 Mice Mimicking the Common Human 13-Base Pair Deletion Mutation Present with Only a Mild Autoimmune Phenotype

(2009) F.-X. Hubert et al.   JOURNAL OF IMMUNOLOGY

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

(2009) Elgene Lim et al.   NATURE MEDICINE

Microarray background correction: maximum likelihood estimation for the normal-exponential convolution

(2008) J. D. Silver et al.   BIOSTATISTICS

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

(2008) Mi-Youn Brusniak et al.   BMC BIOINFORMATICS

NuGO contributions to GenePattern

(2008) P. J. De Groot et al.   Genes and Nutrition