FunkyTax-package: Metagenome Functional and Taxonomic Relationships
In genotyper/FunkyTax: Metagenome Functional and Taxonomic Relationships
Description
Details
Author(s)
References
Description
Quantification of relationships between metagenome function abundances across a factor of interest and the microbiome community composition contributing to each function's frequency.
Details
Use TaFuR to parse a matrix of functions by OTUs by samples into individual community matrices for each function. Resulting matrices include only OTUs contributing to the respective function. TaFuR also performs Hellinger transformations (Legendre and Gallagher 2001) on the matrices, computes corresponding distance matrices, and performs ADONIS. Use CatFun to compare these results with those from DESeq2 (Love et al. 2014) to classify functions and community subsets into functional community categories.
Author(s)
Caleb D. Phillips
Maintainer: Caleb D. Phillips <caleb.phillips@ttu.edu>
References
Anderson, MJ (2001) A new method for non-parametric multivariate analysis of variance, Austral Ecology, 26: 32–46.
Legendre P, Gallagher ED (2001) Ecologically meaningful transformation ofr ordication of species data, Oecologia. 129:271-280.
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biology, 15:550.
Phillips CD, Hanson J, Wilkinson J, Koenig L, Rees E, Webala P, Kingston T (submitted) Microbiome structural and functional incongruence explained along host dietary niche space.
genotyper/FunkyTax documentation built on May 17, 2019, 1:11 a.m.
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Description Details Author(s) References
Description
Quantification of relationships between metagenome function abundances across a factor of interest and the microbiome community composition contributing to each function's frequency.
Details
Use TaFuR to parse a matrix of functions by OTUs by samples into individual community matrices for each function. Resulting matrices include only OTUs contributing to the respective function. TaFuR also performs Hellinger transformations (Legendre and Gallagher 2001) on the matrices, computes corresponding distance matrices, and performs ADONIS. Use CatFun to compare these results with those from DESeq2 (Love et al. 2014) to classify functions and community subsets into functional community categories.
Author(s)
Caleb D. Phillips
Maintainer: Caleb D. Phillips <caleb.phillips@ttu.edu>
References
Anderson, MJ (2001) A new method for non-parametric multivariate analysis of variance, Austral Ecology, 26: 32–46.
Legendre P, Gallagher ED (2001) Ecologically meaningful transformation ofr ordication of species data, Oecologia. 129:271-280.
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biology, 15:550.
Phillips CD, Hanson J, Wilkinson J, Koenig L, Rees E, Webala P, Kingston T (submitted) Microbiome structural and functional incongruence explained along host dietary niche space.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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