DOI: 10.18129/B9.bioc.ccrepe  


Bioconductor version: Release (3.18)

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 <emh146 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>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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biocViews Bioinformatics, ImmunoOncology, Metagenomics, Software, Statistics
Version 1.38.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 years)
License MIT + file LICENSE
Imports infotheo (>= 1.1)
Suggests knitr, BiocStyle, BiocGenerics, testthat
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