eudysbiome

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2

Cartesian plot and contingency test on 16S Microbial data

Bioconductor version: Development (3.24)

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")):

Xiaoyuan Zhou, Christine Nardini. eudysbiome: Cartesian plot and contingency test on 16S Microbial data. doi:10.18129/B9.bioc.eudysbiome, R package version 1.43.0, https://bioconductor.org/packages/eudysbiome.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Software
Version	1.43.0
In Bioconductor since	BioC 3.2 (R-3.2) (11 years)
License	GPL-2
Depends	R (>= 3.1.0)
Imports	plyr, Rsamtools, R.utils, Biostrings
System Requirements
URL

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Build Report	Build Report, r-universe

Package Archives

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

Source Package	eudysbiome_1.43.0.tar.gz
Windows Binary (x86_64)	eudysbiome_1.43.0.zip
macOS Binary (big-sur-x86_64)	eudysbiome_1.43.0.tgz
macOS Binary (sonoma-arm64)	eudysbiome_1.43.0.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