Package: MCMC.OTU
Type: Package
Title: Bayesian Analysis of Multivariate Counts Data in DNA
Metabarcoding and Ecology
Version: 1.0.10
Date: 2016-02-10
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Description: Poisson-lognormal generalized linear mixed model analysis of multivariate counts data using MCMC, aiming to infer the changes in relative proportions of individual variables. The package was originally designed for sequence-based analysis of microbial communities ("metabarcoding", variables = operational taxonomic units, OTUs), but can be used for other types of multivariate counts, such as in ecological applications (variables = species). The results are summarized and plotted using 'ggplot2' functions. Includes functions to remove sample and variable outliers and reformat counts into normalized log-transformed values for correlation and principal component/coordinate analysis. Walkthrough and examples: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/walkthroughExample_mcmcOTU_R.txt.
License: GPL-3
Depends: MCMCglmm, ggplot2, coda
NeedsCompilation: no
Packaged: 2016-02-11 19:23:29 UTC; c-monstr
Repository: CRAN
Date/Publication: 2016-02-12 00:53:04
Package: MCMC.qpcr
Type: Package
Title: Bayesian Analysis of qRT-PCR Data
Version: 1.2.2
Date: 2015-10-26
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Description: Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: http://bit.ly/1Nwo4CB.
License: GPL-3
Depends: MCMCglmm, ggplot2, coda
NeedsCompilation: no
Packaged: 2015-10-28 00:10:05 UTC; c-monstr
Repository: CRAN
Date/Publication: 2015-10-28 08:44:52
Package: pedantics
Type: Package
Title: Functions to facilitate power and sensitivity analyses for
genetic studies of natural populations
Version: 1.5
Date: 2014-01-23
Depends: R (>= 2.4.0), MasterBayes, MCMCglmm, kinship2, grid
Author: Michael Morrissey
Maintainer: Michael Morrissey <michael.morrissey@st-andrews.ac.uk>
Description: Contains functions for sensitivity and power analysis, for calculating statistics describing pedigrees from wild populations, and for viewing pedigrees
License: GPL-2 | GPL-3
LazyLoad: yes
Packaged: 2014-01-23 11:20:39 UTC; michael
Repository: CRAN
Date/Publication: 2014-01-23 12:49:51
NeedsCompilation: yes
providing 
.