We do not have a tradition for package announcements on Bioconductor (except the summary of new packages at release time) which I think is too bad. A while ago, we uploaded cqn (Conditional Quantile Normalization) to Bioconductor devel. The package is an implementation of a method for normalizing RNA-Seq data, represented in a region (gene/exon) by sample matrix. The methodology is described in the following preprint: Hansen, K.D., Irizarry, R.A. & Wu, Z. Removing technical variability in rna-seq data using conditional quantile normalization. Johns Hopkins University, Dept of Biostatistics Working Papers, 227 (2011). http://www.bepress.com/jhubiostat/paper227 Kasper Daniel Hansen, Rafael Irizarry and Zhijin (Jean) Wu