To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("metagenomeSeq")

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

metagenomeSeq

 

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 umiacs.umd.edu>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("metagenomeSeq")

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, 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
LinkingTo
Suggests annotate, BiocGenerics, biom, knitr, gss, RUnit, vegan, interactiveDisplay
SystemRequirements
Enhances
URL https://github.com/nosson/metagenomeSeq/
BugReports https://github.com/nosson/metagenomeSeq/issues
Depends On Me msd16s
Imports Me
Suggests Me interactiveDisplay
Build Report  

Package Archives

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Package Source metagenomeSeq_1.10.0.tar.gz
Windows Binary metagenomeSeq_1.10.0.zip
Mac OS X 10.6 (Snow Leopard) metagenomeSeq_1.10.0.tgz
Mac OS X 10.9 (Mavericks) metagenomeSeq_1.10.0.tgz
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