To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

ccrepe

ccrepe_and_nc.score

Bioconductor version: Release (2.14)

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>

Citation (from within R, enter citation("ccrepe")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ccrepe")

 

PDF R Script ccrepe
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Metagenomics, Software, StatisticalMethod
Version 1.0.0
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 Archives

Follow Installation instructions to use this package in your R session.

Package Source ccrepe_1.0.0.tar.gz
Windows Binary ccrepe_1.0.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ccrepe_1.0.0.tgz
Mac OS X 10.9 (Mavericks) ccrepe_1.0.0.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center