To install this package, start R and enter:

## try http if https is not available

In most cases, you don't need to download the package archive at all.



Statistical analysis for sparse high-throughput sequencing

Bioconductor version: Release (3.1)

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, Hisham Talukder, Mihai Pop, Hector Corrada Bravo

Maintainer: Joseph N. Paulson <jpaulson at>

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


To install this package, start R and enter:

## try http if https is not available


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



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


biocViews Classification, Clustering, DifferentialExpression, GeneticVariability, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization
Version 1.10.0
In Bioconductor since BioC 2.12 (R-3.0) (2.5 years)
License Artistic-2.0
Depends R (>= 3.0), Biobase, limma, methods, RColorBrewer
Imports parallel, matrixStats, gplots
Suggests annotate, BiocGenerics, biom, knitr, gss, RUnit, vegan, interactiveDisplay
Depends On Me msd16s
Imports Me
Suggests Me interactiveDisplay
Build Report  

Package Archives

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

Package Source metagenomeSeq_1.10.0.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard) metagenomeSeq_1.10.0.tgz
Mac OS X 10.9 (Mavericks) metagenomeSeq_1.10.0.tgz
Subversion source (username/password: readonly)
Git source
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center