philr

DOI: 10.18129/B9.bioc.philr    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see philr.

Phylogenetic partitioning based ILR transform for metagenomics data

Bioconductor version: 3.8

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

Maintainer: Justin Silverman <jsilve24 at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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	1.8.1
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 years)
License	GPL-3
Depends
Imports	ape, phangorn, tidyr, ggplot2, ggtree
LinkingTo
Suggests	testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr
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_1.8.1.tar.gz
Windows Binary	philr_1.8.1.zip
Mac OS X 10.11 (El Capitan)	philr_1.8.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/philr
Source Repository (Developer Access)	git clone [email protected]:packages/philr
Package Short Url	http://bioconductor.org/packages/philr/
Package Downloads Report	Download Stats