metagenomeSeq

Statistical analysis for sparse high-throughput sequencing

Bioconductor version: Development (3.0)

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, Mihai Pop, Hector Corrada Bravo

Maintainer: Joseph N. Paulson <jpaulson at umiacs.umd.edu>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("metagenomeSeq")

Documentation

PDF R Script metagenomeSeq: statistical analysis for sparse high-throughput sequencing
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, Metagenomics, Software, Visualization
Version 1.7.0
In Bioconductor since BioC 2.12 (R-3.0)
License Artistic-2.0
Depends R (>= 3.0), Biobase, limma, matrixStats, methods, RColorBrewer, gplots
Imports
Suggests annotate, biom, parallel, vegan, knitr
System Requirements
URL http://cbcb.umd.edu/software/metagenomeSeq
Depends On Me
Imports Me
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Package Downloads

Package Source metagenomeSeq_1.7.0.tar.gz
Windows Binary metagenomeSeq_1.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) metagenomeSeq_1.7.0.tgz
Mac OS X 10.9 (Mavericks)
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