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 pvalues to similarity measures between the microbes. The package has two functions: ccrepe: Calculates similarity measures, pvalues and qvalues for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates specieslevel covariation and coexclusion patterns based on an extension of the checkerboard score to ordinal data.
Package details 


Author  Emma Schwager <emh146@mail.harvard.edu>,Craig Bielski<craig.bielski@gmail.com>, George Weingart<george.weingart@gmail.com> 
Bioconductor views  Bioinformatics Metagenomics Software Statistics 
Maintainer  Emma Schwager <emma.schwager@gmail.com>,Craig Bielski<craig.bielski@gmail.com>, George Weingart<george.weingart@gmail.com> 
License  MIT + file LICENSE 
Version  1.12.0 
Package repository  View on Bioconductor 
Installation 
Install the latest version of this package by entering the following in R:

Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.