(documentation, dowload)

RSEQtools RSEQtools includes a format specification for RNA-Seq data that provides "confidentially-aware" data summaries as well as several tools for performing common analyses: expression measurements (e.g. RPKMs), creation of signal tracks, segmentation, annotation manipulations, etc. RSEQtools
IQSeq IQSeq is a tool for isoform quantification with RNA-Seq data. Given isoform annotation and alignment of RNA-Seq reads, it will use EM algorithm to infer the most probable expression level for each isoform of a gene. IQSeq
FusionSeq FusionSeq is a computational platform to identify fusion transcripts from Paired-End RNA-Seq data. It provides a filtration mechanism to exclude candiates that might have been generated by several sources of noise, such as misalignment or random pairing of transcript fragments during sample preparation. It also ranks the fusion candidates according to several scores to prioritize experimental validation. FusionSeq
ACT (Aggregation and Correlation Toolbox) ACT is a toolbox for harvesting useful results from a vast sea of genomic experimental data. In particular, it is a set of scripts (Aggregation, Correlation, and Saturation) designed to be downloaded and used to analyze signal or hit tracks. ACT