ccrepe

ccrepe_and_nc.score

Bioconductor version: Development (3.0)

The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets. In microbial abundance data, for example, the total abundances of all microbes sum to one; CCREPE is designed to take this constraint into account when assigning p-values to similarity measures between the microbes. The package has two functions: ccrepe: Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data.

Author: Emma Schwager <emma.schwager at gmail.com>,Craig Bielski<craig.bielski at gmail.com>, George Weingart<george.weingart at gmail.com>

Maintainer: Emma Schwager <emma.schwager at gmail.com>,Craig Bielski<craig.bielski at gmail.com>, George Weingart<george.weingart at gmail.com>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("ccrepe")

To cite this package in a publication, start R and enter:

    citation("ccrepe")

Documentation

PDF R Script ccrepe
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Metagenomics, Software, StatisticalMethod
Version 1.1.0
In Bioconductor since BioC 2.14 (R-3.1)
License MIT + file LICENSE
Depends
Imports infotheo (>= 1.1)
Suggests knitr, BiocStyle, BiocGenerics
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source ccrepe_1.1.0.tar.gz
Windows Binary ccrepe_1.1.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ccrepe_1.1.0.tgz
Mac OS X 10.9 (Mavericks)
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