Package: ccrepe
Type: Package
Title: ccrepe_and_nc.score
Version: 1.22.0
Imports: infotheo (>= 1.1)
Date: 2014-10-29
Author: Emma Schwager <emh146@mail.harvard.edu>,Craig Bielski<craig.bielski@gmail.com>, George Weingart<george.weingart@gmail.com>
Maintainer: Emma Schwager <emma.schwager@gmail.com>,Craig Bielski<craig.bielski@gmail.com>, George Weingart<george.weingart@gmail.com>
Description: 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.
License: MIT + file LICENSE
VignetteBuilder: knitr
Suggests: knitr, BiocStyle, BiocGenerics, testthat
biocViews: ImmunoOncology, Statistics, Metagenomics, Bioinformatics,
        Software
git_url: https://git.bioconductor.org/packages/ccrepe
git_branch: RELEASE_3_10
git_last_commit: 1c05f01
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
NeedsCompilation: no
Packaged: 2019-10-30 02:25:56 UTC; biocbuild
Built: R 3.6.1; ; 2019-10-30 12:50:23 UTC; windows
