metagenomeSeq
This is the development version of metagenomeSeq; for the stable release version, see metagenomeSeq.
Statistical analysis for sparse high-throughput sequencing
Bioconductor version: Development (3.21)
metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.
Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Maintainer: Joseph N. Paulson <josephpaulson at gmail.com>
citation("metagenomeSeq")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("metagenomeSeq")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
Reference Manual |
Details
biocViews | Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization |
Version | 1.49.0 |
In Bioconductor since | BioC 2.12 (R-3.0) (11.5 years) |
License | Artistic-2.0 |
Depends | R (>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer |
Imports | parallel, matrixStats, foreach, Matrix, gplots, graphics, grDevices, stats, utils, Wrench |
System Requirements | |
URL | https://github.com/nosson/metagenomeSeq/ |
Bug Reports | https://github.com/nosson/metagenomeSeq/issues |
See More
Suggests | annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | |
Windows Binary (x86_64) | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/metagenomeSeq |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/metagenomeSeq |
Package Short Url | https://bioconductor.org/packages/metagenomeSeq/ |
Package Downloads Report | Download Stats |