ccrepe

DOI: 10.18129/B9.bioc.ccrepe    

ccrepe_and_nc.score

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("ccrepe")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ccrepe")

 

PDF	R Script	ccrepe
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bioinformatics, ImmunoOncology, Metagenomics, Software, Statistics
Version	1.28.0
In Bioconductor since	BioC 2.14 (R-3.1) (7.5 years)
License	MIT + file LICENSE
Depends
Imports	infotheo (>= 1.1)
LinkingTo
Suggests	knitr, BiocStyle, BiocGenerics, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ccrepe_1.28.0.tar.gz
Windows Binary	ccrepe_1.28.0.zip
macOS 10.13 (High Sierra)	ccrepe_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ccrepe
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ccrepe
Package Short Url	https://bioconductor.org/packages/ccrepe/
Package Downloads Report	Download Stats