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ccrepe

This is the development version of ccrepe; for the stable release version, see ccrepe.

ccrepe_and_nc.score

Bioconductor version: Development (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 mail.harvard.edu>,Craig Bielski<craig.bielski at gmail.com>, George Weingart<george.weingart at gmail.com>

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

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

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ccrepe")

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

Documentation

Reference Manual PDF

Details

biocViews Bioinformatics, ImmunoOncology, Metagenomics, Software, Statistics
Version 1.37.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 years)
License MIT + file LICENSE
Depends
Imports infotheo (>= 1.1)
Linking To
Suggests knitr, BiocStyle, BiocGenerics, testthat
System Requirements
Enhances
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Depends On Me
Imports Me
Suggests Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary ccrepe_1.37.0.zip
macOS Binary (x86_64) ccrepe_1.37.0.tgz
macOS Binary (arm64) ccrepe_1.37.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ccrepe
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ccrepe
Bioc Package Browser https://code.bioconductor.org/browse/ccrepe/
Package Short Url https://bioconductor.org/packages/ccrepe/
Package Downloads Report Download Stats