OK, so I just ‘found‘ shiny and it has a lot of cool stuff to it. OK, I’ve known about it for a long time but have just had the opportunity to sit down and work it out and see how it can fit into the presentation and learning I’m trying to develop in my Applied Population Genetics online textbook. Here is a brief overview of how I set up the shiny server on my Ubuntu box that is hosting the book (so I can embed more interactivity in the display).
The analysis of genetic marker data is increasingly being conducted in the context of the spatial arrangement of strata (e.g. populations) necessitating a more flexible set of analysis tools. GeneticStudio consists of four interacting programs: (i) Geno a spreadsheet-like interface for the analysis of spatially explicit marker-based genetic variation; (ii) Graph software for the analysis of Population Graph and network topologies, (iii) Manteller, a general purpose for matrix analysis program; and (iv) SNPFinder, a program for identifying single nucleotide polymorphisms. The GeneticStudio suite is available as source code as well as binaries for OSX and Windows and is distributed under the GNU General Public License.
The server-based program GENER performs the two-generation analysis of pollen flow for data consisting of mother/offspring arrays using genetic markers. The GENER program decomposes the genetic variance sampled by maternal individuals within and among pollen pool components of genetic variance and is accessible from http://dyerlab.bio.vcu.edu. These estimates are used to construct the test statistic, Φft, whose significance is tested via permutation. The Φft statistic can subsequently be used to quantify genetic effective pollen donor population size (Nep), effective mating area and dispersal distance. Furthermore, the GENER program can calculate Φft values for all pairs of substrata within the data set.