Re:Show HN: PyGeno, a Python Package for Precision Medicine
by daoudat on Tuesday February 23, 2016 @03:00PM
(#11161814)
Actually it's not. It has been written from scratch including the ORM that runs in the background (https://github.com/tariqdaouda/rabaDB). The goal was to have a powerful optimized tool with 0 dependencies that can be easily deployed on any platform.
It was designed to be flexible and powerful enough to be appealing to both bioinformaticians and casual users, and it used daily here at the Institute for Research in Immunology and Cancer (www.iric.ca) by professional bioinformaticians, as well as biologists who have learned to program using it.
PyGeno was already used for two peer reviewed articles:
-Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides. Granados, Sriranganadane, Daouda et al. 2014, Nat. Comm
-MHC I-associated peptides preferentially derive from transcripts bearing miRNA response elements. Granados et al. 2012, Blood
And four others are on the way.
I feel like this might not be sophisticated enough for bioinformaticians, but too complex for the casual user or clinician. Unfortunately, proper bioinformatics requires a heafty dose of background knowledge. If you don't understand what you are aligning and filtering, and why, then the results will always just be a shot in the dark.