MCMC.qpcr

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

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MCMC.qpcr' ...
** package 'MCMC.qpcr' successfully unpacked and MD5 sums checked
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MCMC.qpcr'
    finding HTML links ... done
    HPDplot                                 html  
    HPDplotBygene                           html  
    HPDplotBygeneBygroup                    html  
    HPDpoints                               html  
    HPDsummary                              html  
    MCMC.qpcr-package                       html  
    PrimEff                                 html  
    amp.eff                                 html  
    beckham.data                            html  
    beckham.eff                             html  
    coral.stress                            html  
    cq2counts                               html  
    cq2genorm                               html  
    cq2log                                  html  
    diagnostic.mcmc                         html  
    dilutions                               html  
    getNormalizedData                       html  
    mcmc.converge.check                     html  
    mcmc.pval                               html  
    mcmc.qpcr                               html  
    mcmc.qpcr.classic                       html  
    mcmc.qpcr.lognormal                     html  
    normalize.qpcr                          html  
    outlierSamples                          html  
    padj.qpcr                               html  
    softNorm                                html  
    summaryPlot                             html  
    trellisByGene                           html  
** building package indices
** testing if installed package can be loaded
* DONE (MCMC.qpcr)
Making 'packages.html' ... done