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.
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
0.1.3 |
rolling linux/jammy R-4.5 | holobiont_0.1.3.tar.gz |
28.9 KiB |
0.1.3 |
rolling linux/noble R-4.5 | holobiont_0.1.3.tar.gz |
28.9 KiB |
0.1.3 |
rolling source/ R- | holobiont_0.1.3.tar.gz |
28.9 KiB |
0.1.3 |
latest linux/jammy R-4.5 | holobiont_0.1.3.tar.gz |
28.9 KiB |
0.1.3 |
latest linux/noble R-4.5 | holobiont_0.1.3.tar.gz |
28.9 KiB |
0.1.3 |
latest source/ R- | holobiont_0.1.3.tar.gz |
28.9 KiB |
0.1.3 |
2026-04-26 source/ R- | holobiont_0.1.3.tar.gz |
28.9 KiB |
0.1.3 |
2026-04-23 source/ R- | holobiont_0.1.3.tar.gz |
28.9 KiB |
0.1.2 |
2025-04-20 source/ R- | holobiont_0.1.2.tar.gz |
17.2 KiB |