holobiont: Microbiome Analysis Tools
We provide functions for identifying the core community phylogeny in any microbiome, drawing phylogenetic Venn diagrams, calculating the core Faith’s PD for a set of communities, and calculating the core UniFrac distance between two sets of communities. All functions rely on construction of a core community phylogeny, which is a phylogeny where branches are defined based on their presence in multiple samples from a single type of habitat. Our package provides two options for constructing the core community phylogeny, a tip-based approach, where the core community phylogeny is identified based on incidence of leaf nodes and a branch-based approach, where the core community phylogeny is identified based on incidence of individual branches. We suggest use of the microViz package.
| Version: |
0.1.3 |
| Imports: |
ape, phyloseq, phytools, ggplot2, dplyr, utils, tibble, castor, vegan, data.table |
| Published: |
2025-07-21 |
| DOI: |
10.32614/CRAN.package.holobiont |
| Author: |
Sharon Bewick [aut, cre],
Benjamin Camper [aut],
National Science Foundation Division of Integrative Organismal Systems
(award #2104605) [fnd] |
| Maintainer: |
Sharon Bewick <sbewick at clemson.edu> |
| License: |
GPL-2 |
| NeedsCompilation: |
no |
| CRAN checks: |
holobiont results |
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