Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1211 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. It is expected that emerging digital gene expression (DGE) technologies will overtake Microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for geneexpressionstudies, involves determining whether there is evidence that counts for a transcriptor exon are significantly different across experimental conditions. edger is a Bioconductor software package for examining differential expression of replicated count data. An over dispersed Poisson model is used to account for both over dispersion across transcripts, improving the reliability of Inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data.