RNAseqR

RNAseqR is designed for expression analysis of RNA-seq data, and is best suited for analysis of multiple, unreplicated libraries. It is a C++ coded program currently compiled for Linux systems.

With GUI and command line interfaces, it can do log, PPM, and/or RPKM (if lengths provided) transformations, as well as, statistical analysis for differential expression, using the negative binomial cumulative distribution function (CDF) or the R test statistic introduced for EST analysis by Stekel, et al.

Output allows for decisions based on CDF probabilities, top R values, or comparison of R values with randomized data. Comparisons are the believability metric of Stekel et al, or observed vs expected R at a given mean expression. Randomization is through Poisson or negative binomial distributions, or column shuffling.