Microbiome Analysis Tools

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Documentation for package ‘holobiont’ version 0.1.3

• DESCRIPTION file.

Help Pages

basic_branch	Branch-based Core Community Phylogeny Using Thresholds
basic_np	Non-phylogenetic Core Community Phylogeny Using Thresholds
basic_tip	Tip-based Core Community Phylogeny Using Thresholds
coreEdges	Edges of the Tree Included in the Core Community Phylogeny
coreFaithsPD	Faiths PD of the Core Microbiome
coreJaccard	Jaccard Distance Between Core Microbiomes from Two Habitats
corePhyloVenn	Phylogenetic Venn Diagram Comparing Core Microbiomes from Multiple Habitats
coreRichness	Richness of the Core Microbiome
coreTaxa	Taxa Included in the Core Microbiome
coreTree	The Core Community Phylogeny
coreUniFrac	UniFrac Distance Between Core Microbiomes from Two Habitats
coreVenn	Venn Diagram Comparing (Non-Phylogenetic) Core Microbiomes from Multiple Habitats
coreVennTree	Phylogeny with Branches Colored Based on Venn Diagram
ggvenn2	A modified version of functions from the ggvenn package for plotting phylogenetic venn diagrams.
shade_branch	Branch-based Core Community Phylogeny Using the Shade & Stopnisek (2019) algorithm.
shade_np	Non-phylogenetic Core Community Using the Shade & Stopnisek (2019) algorithm.
shade_tip	Tip-based Core Community Phylogeny Using the Shade & Stopnisek (2019) algorithm.