Package: ccrepe
Type: Package
Title: ccrepe_and_nc.score
Version: 1.47.0
Imports: infotheo (>= 1.1)
Date: 2024-02-06
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, RUnit
biocViews: ImmunoOncology, Statistics, Metagenomics, Bioinformatics,
        Software
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:17:30 UTC
RemoteUrl: https://github.com/bioc/ccrepe
RemoteRef: HEAD
RemoteSha: 2b6c5e9b4d3c4b687f592be5f9232843a0fcef74
NeedsCompilation: no
Packaged: 2025-11-02 03:34:09 UTC; root
Built: R 4.6.0; ; 2025-11-02 03:35:51 UTC; windows
