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.

See also

Useful links:

• https://rmsharp.github.io/nprcgenekeepr/

• https://github.com/rmsharp/nprcgenekeepr

• Report bugs at https://github.com/rmsharp/nprcgenekeepr/issues

Author

Maintainer: R. Mark Sharp rmsharp@me.com (ORCID) [copyright holder, data contributor]

Authors:

• R. Mark Sharp rmsharp@me.com (ORCID) [copyright holder, data contributor]

• Michael Raboin

• Terry Therneau

• Amanda Vinson [data contributor]

• Matthew Schultz (ORCID)

Other contributors:

• Southwest National Primate Research Center (NIH grant P51 RR13986, work up to and including version 1.0) [funder]

• Oregon National Primate Research Center (NIH grant P51 OD011092, work up to and including version 1.0) [funder]