eudysbiome

DOI: 10.18129/B9.bioc.eudysbiome    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see eudysbiome.

Cartesian plot and contingency test on 16S Microbial data

Bioconductor version: 3.13

eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.

Author: Xiaoyuan Zhou, Christine Nardini

Maintainer: Xiaoyuan Zhou <zhouxiaoyuan at picb.ac.cn>

Installation

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

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

BiocManager::install("eudysbiome")

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("eudysbiome")

 

PDF	R Script	eudysbiome User Manual
PDF		Reference Manual
Text		NEWS

Details

biocViews	Software
Version	1.22.0
In Bioconductor since	BioC 3.2 (R-3.2) (6 years)
License	GPL-2
Depends	R (>= 3.1.0)
Imports	plyr, Rsamtools, R.utils, Biostrings
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Package Archives

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

Source Package	eudysbiome_1.22.0.tar.gz
Windows Binary	eudysbiome_1.22.0.zip
macOS 10.13 (High Sierra)	eudysbiome_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/eudysbiome
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/eudysbiome
Package Short Url	https://bioconductor.org/packages/eudysbiome/
Package Downloads Report	Download Stats