» A Bioconductor package to classify putative polyA sites as true or false/internally oligodT primed

Description: cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data. This package uses the naïve Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.

Publication: Sheppard S, Lawson ND* and Zhu LJ*. [* denotes cocorresponding author] Accurate identification of polyadenylation sites from 3' end deep sequencing using a naïve Bayes classifier. Bioinformatics. 2013, 9(20):2564.