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Statistical analysis for sparse high-throughput sequencing

Bioconductor version: Release (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 <josephpaulson at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization
Version 1.46.0
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
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Suggests annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW
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Depends On Me microbiomeExplorer, etec16s
Imports Me benchdamic, Maaslin2, mbQTL, microbiomeDASim, microbiomeMarker, ggpicrust2, MetaLonDA
Suggests Me dar, interactiveDisplay, phyloseq, scTreeViz, Wrench
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Follow Installation instructions to use this package in your R session.

Source Package metagenomeSeq_1.46.0.tar.gz
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macOS Binary (x86_64) metagenomeSeq_1.46.0.tgz
macOS Binary (arm64) metagenomeSeq_1.46.0.tgz
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