philr

DOI: 10.18129/B9.bioc.philr  

Phylogenetic partitioning based ILR transform for metagenomics data

Bioconductor version: Release (3.16)

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 gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("philr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("philr")

 

HTML	R Script	Introduction to PhILR
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version	1.24.0
In Bioconductor since	BioC 3.4 (R-3.3) (6.5 years)
License	GPL-3
Depends
Imports	ape, phangorn, tidyr, ggplot2, ggtree, methods
LinkingTo
Suggests	testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia
SystemRequirements
Enhances
URL	https://github.com/jsilve24/philr
BugReports	https://github.com/jsilve24/philr/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	philr_1.24.0.tar.gz
Windows Binary	philr_1.24.0.zip
macOS Binary (x86_64)	philr_1.24.0.tgz
macOS Binary (arm64)	philr_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/philr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/philr
Bioc Package Browser	https://code.bioconductor.org/browse/philr/
Package Short Url	https://bioconductor.org/packages/philr/
Package Downloads Report	Download Stats