quipu: Summary charts of micro satellite profiles for a set of biological samples

Gene banks increasingly use molecular markers for routine characterization of plant collections and farmer managed diversity. The gene bank of the International Potato Center presently uses a micro-satellite marker kit to produce molecular profiles for potato accessions. We have been searching for a compact graphical representation that shows both molecular diversity and accession characteristics - thus permitting biologists and collection curators to have a simple way to interpret molecular data. Inspired by the ancient Andean data recording system we devised a graph that allows for standardized representation while leaving room for updates of the marker kit and the collection of accessions. The graph has been used in several catalogs of potatoes.

Author
Reinhard Simon, Pablo Carhuapoma, Vilma Hualla, Stef de Haan, Marc Ghislain, Jorge Nunez, Rene Gomez, Felipe de Mendiburu, William Roca, Merideth Bonierbale
Date of publication
2014-04-22 18:49:03
Maintainer
Reinhard Simon <R.SIMON@CGIAR.ORG>
License
GPL-2
Version
1.9.0

View on CRAN

Man pages

allele.freqs
Sample allele frequencies
potato.quipu
SSR sample data for a set of potato accessions
quipu-package
Quipu-type charts for a set of SSR markers.
rquipu
Creates quipu-type charts for a set of SSR markers
runDemo
Run a short interactive demo

Files in this package

quipu
quipu/inst
quipu/inst/examples
quipu/inst/examples/ex_runDemo.R
quipu/inst/examples/rquipu.R
quipu/inst/shiny
quipu/inst/shiny/ui.R
quipu/inst/shiny/server.R
quipu/inst/doc
quipu/inst/doc/Quipu_tutorial.Rnw
quipu/inst/doc/Quipu_tutorial.pdf
quipu/inst/doc/Quipu_tutorial.R
quipu/NAMESPACE
quipu/data
quipu/data/potato.quipu.rda
quipu/data/allele.freqs.rda
quipu/R
quipu/R/quipu.R
quipu/vignettes
quipu/vignettes/Quipu_tutorial.Rnw
quipu/vignettes/Bioconductor.sty
quipu/README.md
quipu/MD5
quipu/build
quipu/build/vignette.rds
quipu/DESCRIPTION
quipu/man
quipu/man/allele.freqs.Rd
quipu/man/quipu-package.Rd
quipu/man/rquipu.Rd
quipu/man/runDemo.Rd
quipu/man/potato.quipu.Rd