metagenomeSeq

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see metagenomeSeq.

Statistical analysis for sparse high-throughput sequencing

Bioconductor version: 3.18

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 <jpaulson at jimmy.harvard.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("metagenomeSeq")

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("metagenomeSeq")

fitTimeSeries: differential abundance analysis through time or location	PDF	R Script
metagenomeSeq: statistical analysis for sparse high-throughput sequencing	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization
Version	1.43.0
In Bioconductor since	BioC 2.12 (R-3.0) (11 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

Suggests	annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW
Linking To
Enhances
Depends On Me	etec16s, microbiomeExplorer, msd16s
Imports Me	benchdamic, Maaslin2, mbQTL, microbiomeDASim, microbiomeMarker
Suggests Me	interactiveDisplay, phyloseq, scTreeViz, Wrench
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	metagenomeSeq_1.43.0.tar.gz
Windows Binary	metagenomeSeq_1.43.0.zip
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
Bioc Package Browser	https://code.bioconductor.org/browse/metagenomeSeq/
Package Short Url	https://bioconductor.org/packages/metagenomeSeq/
Package Downloads Report	Download Stats