alpine

(the Sassolungo mountain in the Dolomites)

alpine is an R/Bioconductor package for modeling and correcting fragment sequence bias for RNA-seq transcript abundance estimation. In particular, it is the first method of its kind to take into account sample-specific dependence of RNA-seq fragments on their GC content.

An example workflow can be found in vignettes/alpine.Rmd, or by typing:

vignette("alpine")

alpine is designed for un-stranded paired-end RNA-seq data.

A paper explaining the alpine methods was published in December 2016:

http://dx.doi.org/10.1038/nbt.3682