[Bioc-devel] JunctionSeq Release

Hartley, Stephen (NIH/NHGRI) [F] stephen.hartley at nih.gov
Thu Feb 4 19:10:03 CET 2016

So the acceptance email from the package maintainer said "we strongly encourage you to send a note to Bioc-devel to announce its public availability (with a short description) so other people can start to test it." Oddly, however, I've never actually seen anyone post such mail to this list.

But here goes:

My package, JunctionSeq, is now available for use on the devel branch.

JunctionSeq is a tool designed to detect differential usage of exons and splice junctions (including novel splice junctions) as a proxy for detecting differential isoform usage. The statistical method is based on the DEXSeq methodology, with substantial modification. Querying splice junctions substantially improves detection of differential usage, particularly when operating on low-quality or incomplete transcript annotations. JunctionSeq also has a powerful visualization toolkit with a large number of major refinements intended to improve the readability and accessibility of the results. This is particularly critical for this sort of analysis, as alternative splicing can be exceedingly complex and counterintuitive.

You can find the JunctionSeq Bioconductor page here: http://bioconductor.org/packages/JunctionSeq/. I also still have a github-pages-style webpage here: http://hartleys.github.io/JunctionSeq/, which includes fancy knitr-generated static html help docs (http://hartleys.github.io/JunctionSeq/Rhtml/index.html), along with example data bam files and a comprehensive analysis pipeline walkthrough.

Steve Hartley

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