LOX: inferring Level Of eXpression from diverse methods of census sequencing

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

(2009) Likun Wang et al.   BIOINFORMATICS

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

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

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

(2009) Joshua S Bloom et al.   BMC GENOMICS

Expression profiling of microRNAs by deep sequencing

(2009) C. J. Creighton et al.   BRIEFINGS IN BIOINFORMATICS

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH