RNA-Seq

srnadiff is a R/BioConductor package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation.

mmquant is a RNA-Seq quantification tool, with a dedicated quantification of multiple-mapping reads. While mmquant is developped in C++, the R binding is available from Rmmquant BioConductor repository.

RNAseqNet is an R package that implements network inference with log-linear Poisson Graphical Model. Hot-deck multiple imputation method can be used to improve the reliability of the inference with an auxiliary dataset.