GStudio: An R Package for Spatial Analysis of Marker Data

This is the main package that provides data types and routines for spatial analysis of genetic marker data. The previous version is currently available on CRAN and you can install it rom within your R environtment by invoking the command

install.packages("gstudio")

If you want to keep up with the latest developments of this package, you can use the version found on GitHub.  Install it from within R as:

require(devtools)
install_github("dyerlab/gstudio")

and that should get you up-to-date.  You’ll need to have a fully working LaTeX install and some other stuff to build it if you fork.

The Users Manual for the package with several examples can be found here

I have started a github account for this package, you can get access to the whole codebase read about it on the wiki, and contribute to the project from its repo at https://github.com/dyerlab.

Garrick RC, Meadows CA, Nason JD, Cognato AI, Dyer RJ. 2009. Variable markers for a Sonoran dessert bark beetle, Araptus attenuatus Wood (Curculionidae:Scolytinae), with applications to related genera. Conservation Genetics, 10 1177-1179.

Garrick RC, Meadows CA, Nason JD, Cognato AI, Dyer RJ. 2009. Variable markers for a Sonoran dessert bark beetle, Araptus attenuatus Wood (Curculionidae:Scolytinae), with applications to related genera. Conservation Genetics, 10 1177-1179.

We report eight new co-dominant nuclear markers for population genetics of the bark beetle Araptus attenuatus Wood. Several loci include introns from low- copy genes, and four cross-amplify in one or more related genera. The markers show moderate levels of polymorphism (2–19 alleles per locus), and no loci showed significant deviations from Hardy–Weinberg or linkage equilibrium across both of the two populations examined, consistent with Mendelian inheritance patterns.

DOI: 10.1007/s10592-008-9738-3

Garrick RC, Meadows CA, Nicolas AN, Nason JD, Dyer RJ. 2008. A set of polymorphic nuclear intron markers for conservation genetics and phylogeography of Euphorbia species (Pedilanthus clade). Conservation Genetics, 9 1673-1676.

Garrick RC, Meadows CA, Nicolas AN, Nason JD, Dyer RJ. 2008. A set of polymorphic nuclear intron markers for conservation genetics and phylogeography of Euphorbia species (Pedilanthus clade). Conservation Genetics, 9 1673-1676.

We developed seven nuclear intron markers for Euphorbia lomelii. New exon-primed intron-crossing (EPIC) oligonucleotides were used for initial amplification and sequencing, then locus-specific primers and restriction fragment length polymorphism genotyping assays were designed. Loci showed no significant deviation from Hardy–Weinberg and linkage equilibrium, and they cross-amplify in at least three congeneric species.

DOI: 10.1007/s10592-008-9521-5