eudysbiome
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see eudysbiome.
Cartesian plot and contingency test on 16S Microbial data
Bioconductor version: 3.7
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("eudysbiome")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("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")| eudysbiome User Manual | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Software |
| Version | 1.10.0 |
| 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 |
| System Requirements | |
| URL |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | eudysbiome_1.10.0.tar.gz |
| Windows Binary | eudysbiome_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | eudysbiome_1.10.0.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 |
| Old Source Packages for BioC 3.7 | Source Archive |