DOI: 10.18129/B9.bioc.philr  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see philr.

Phylogenetic partitioning based ILR transform for metagenomics data

Bioconductor version: 3.17

PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.

Author: Justin Silverman [aut, cre], Leo Lahti [ctb]

Maintainer: Justin Silverman <jsilve24 at>

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biocViews ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version 1.26.0
In Bioconductor since BioC 3.4 (R-3.3) (7 years)
License GPL-3
Imports ape, phangorn, tidyr, ggplot2, ggtree, methods
Suggests testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia
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