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nprcgenekeepr: Genetic Tools for Colony Management
Provides genetic tools for colony management and is 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' 'mulatto')". It provides a 'Shiny' application with an exposed API. The application supports five 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.
Getting started
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Package details |
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| Author | Michael Raboin [aut], Terry Therneau [aut], Amanda Vinson [aut, dtc], R. Mark Sharp [aut, cre, cph, dtc] (<https://orcid.org/0000-0002-6170-6942>), Matthew Schultz [aut] (<https://orcid.org/0000-0001-5103-4305>), Southwest National Primate Research Center NIH grant P51 RR13986 [fnd], Oregon National Primate Research Center grant P51 OD011092 [fnd] |
| Maintainer | R. Mark Sharp <rmsharp@me.com> |
| License | MIT + file LICENSE |
| Version | 1.0.7 |
| URL | https://rmsharp.github.io/nprcgenekeepr/ https://github.com/rmsharp/nprcgenekeepr |
| Package repository | View on CRAN |
| Installation |
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