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>,Craig Bielski<craig.bielski at>, George Weingart<george.weingart at>

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

To install this package, start R and enter:


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


PDF R Script ccrepe
PDF   Reference Manual
Text   NEWS


biocViews Metagenomics, Software, StatisticalMethod
Version 1.0.0
In Bioconductor since BioC 2.14 (R-3.1)
License MIT + file LICENSE
Imports infotheo (>= 1.1)
Suggests knitr, BiocStyle, BiocGenerics
System Requirements
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source ccrepe_1.0.0.tar.gz
Windows Binary (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
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