nprcgenekeepr - Genetic Tools for Colony Management
Provides genetic tools for colony management and
implements a derivation of the work in Amanda Vinson and
Michael J Raboin (2015)
<https://pmc.ncbi.nlm.nih.gov/articles/PMC4671785/> "A
Practical Approach for Designing Breeding Groups to Maximize
Genetic Diversity in a Large Colony of Captive Rhesus Macaques
('Macaca' 'mulatta')". It provides a 'Shiny' application with
an exposed API. The application supports these main groups of
functions: (1) Quality control of studbooks contained in text
files or 'Excel' workbooks and of pedigrees within 'LabKey'
Electronic Health Records (EHR); (2) Creation of pedigrees from
a list of animals using the 'LabKey' EHR integration; (3)
Creation and display of an age by sex pyramid plot of the
living animals within the designated pedigree; (4) Generation
of genetic value analysis reports; and (5) Creation of
potential breeding groups with and without proscribed sex
ratios and defined maximum kinships. Further tabs cover mate
pair analysis, genetic diversity, marker genetics, potential
parents, cross-center identity mapping, de-identified export,
and genetic-health trends.
