EAMA: Empirically adjusted meta-analysis for large-scale simultaneous hypothesis testing in genomic experiments

SimSeq: a nonparametric approach to simulation of RNA-sequence datasets

(2015) Sam Benidt et al.   BIOINFORMATICS

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

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

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge

(2013) Adi L. Tarca et al.   BIOINFORMATICS

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Ectopic Activation of Germline and Placental Genes Identifies Aggressive Metastasis-Prone Lung Cancers

(2013) S. Rousseaux et al.   Science Translational Medicine

Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: With application to major depressive disorder

(2012) Xingbin Wang et al.   BMC BIOINFORMATICS

Relation between smoking history and gene expression profiles in lung adenocarcinomas

(2012) Johan Staaf et al.   BMC Medical Genomics

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

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

METAL: fast and efficient meta-analysis of genomewide association scans

(2010) C. J. Willer et al.   BIOINFORMATICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH