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Generalized UniFrac
eagle-i ID
http://eagle-i.itmat.upenn.edu/i/0000013a-c2c1-63a1-d69a-d90d80000000
Resource Type
Properties
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Resource Description
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The human microbiome plays an important role in human disease and health. Identification of factors that affect the microbiome composition can provide insights into disease mechanism as well as suggest ways to modulate the microbiome composition for therapeutical purposes. Distance-based statistical tests have been applied to test the association of microbiome composition with environmental or biological covariates. The unweighted and weighted UniFrac distances are the most widely used distance measures. However, these two measures assign too much weight either to rare lineages or to most abundant lineages, which can lead to loss of power when the important composition change occurs in moderately abundant lineages.
We develop generalized UniFrac distances that extend the weighted and unweighted UniFrac distances for detecting a much wider range of biologically relevant changes.
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Additional Name
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GUniFrac
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Used by
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Statistical Genetics and Genomics Laboratory
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Version
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1.0
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Data Input
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Rooted phylogenetic tree of R class "phylo"
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Data Input
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Operational taxonomic unit count table
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Data Output
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Generalized UniFrac distances
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Related Publication or Documentation
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Associating microbiome composition with environmental covariates using generalized UniFrac distances
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Website(s)
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http://cran.r-project.org/web/packages/GUniFrac/index.html
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Related Technique
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Metagenomics analysis
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Developed by
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Li, Hongzhe., PhD
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Software license
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GNU General Public License
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Coded in
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R language
