metagenomeSeq

DOI: 10.18129/B9.bioc.metagenomeSeq    

Statistical analysis for sparse high-throughput sequencing

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization
Version	1.38.0
In Bioconductor since	BioC 2.12 (R-3.0) (9.5 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
LinkingTo
Suggests	annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW
SystemRequirements
Enhances
URL	https://github.com/nosson/metagenomeSeq/
BugReports	https://github.com/nosson/metagenomeSeq/issues
Depends On Me	etec16s, metavizr, microbiomeExplorer, msd16s
Imports Me	benchdamic, Maaslin2, microbiomeDASim, microbiomeMarker
Suggests Me	interactiveDisplay, phyloseq, scTreeViz, Wrench
Links To Me
Build Report

Package Archives

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

Source Package	metagenomeSeq_1.38.0.tar.gz
Windows Binary	metagenomeSeq_1.38.0.zip
macOS Binary (x86_64)	metagenomeSeq_1.38.0.tgz
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