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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see metagenomeSeq.

Statistical analysis for sparse high-throughput sequencing

Bioconductor version: 3.4

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")):


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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 1.16.0
In Bioconductor since BioC 2.12 (R-3.0) (4 years)
License Artistic-2.0
Depends R (>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer
Imports parallel, matrixStats, foreach, Matrix, gplots
Suggests annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay
Depends On Me etec16s, msd16s
Imports Me metagenomeFeatures
Suggests Me interactiveDisplay, phyloseq
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