Package: biotyper
Type: Package
Title: biotyper: an R package to biotype a community
Version: 0.1.3
Depends: R (>= 1.8.0), ade4, fpc, clusterSim
Date: 2020-08-27
Author: Julien Tap, Daniel R. Mende
Maintainer: Julien Tap jtap@jouy.inra.fr, Daniel R. Mende mende@embl.de
Contributor: John Bouranis @bouranij
Description: This package provide numerous functions for biotyping your community dataset based on clustering and classification techniques.
License: GPL 2
LazyLoad: yes
Short story : package developped for the enterotype paper (Arumugam et al., Nature, 2010) at EMBL. I am still maintain it at Danone Nutricia Research hoping that it could be useful for other users too. more information with the enterotype tutorial : http://enterotype.embl.de/. A more recent method to cluster enterotypes using reference-based assignments can be found here http://enterotypes.org/
Install : you can install the BiotypeR package from GitHub using devtools package.
require(devtools)
install_github("tapj/BiotypeR")
library(BiotypeR)
data(Titanium16S)
Titanium16S.biotypes=biotyper.data.frame(Titanium16S, k=3, manalysis=TRUE)