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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 (3.19)

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 "4.4") 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

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

Details

biocViews Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization
Version 1.45.0
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
See More
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 dar, 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_1.45.0.tar.gz
Windows Binary
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