alpine has moved to Bioconductor (8/18/2016)

Furthermore, the version here is already out-of-date. The version at Bioconductor has a simplified interface.

I will still use the GitHub Issues tracker for new feature ideas & TODOs, but the new website for alpine is:

http://bioconductor.org/packages/alpine

New feature requests can be submitted as Issues here on GitHub.

Bug reports and any other support questions should be posted to:

http://support.bioconductor.org

(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.

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

vignette("alpine")

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

A manuscript explaining the alpine methods and the background behind fragment sequence bias is posted to bioRxiv.