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eudysbiome

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

Cartesian plot and contingency test on 16S Microbial data


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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

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")
eudysbiome User Manual PDF R Script
Reference Manual PDF

Details

biocViews Software
Version 1.33.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 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_1.33.0.tar.gz
Windows Binary
macOS Binary (x86_64) eudysbiome_1.33.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/eudysbiome
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/eudysbiome
Bioc Package Browser https://code.bioconductor.org/browse/eudysbiome/
Package Short Url https://bioconductor.org/packages/eudysbiome/
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