philr

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see philr.

Phylogenetic partitioning based ILR transform for metagenomics data

Bioconductor version: 3.13

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>

Citation (from within R, enter citation("philr")):

Installation

To install this package, start R (version "4.1") 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")

Introduction to PhILR HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software

Version 1.18.0

In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)

License GPL-3

Depends

Imports ape, phangorn, tidyr, ggplot2, ggtree

System Requirements

URL https://github.com/jsilve24/philr

Bug Reports https://github.com/jsilve24/philr/issues

Suggests testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package philr_1.18.0.tar.gz

Windows Binary philr_1.18.0.zip

macOS 10.13 (High Sierra) philr_1.18.0.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

Old Source Packages for BioC 3.13 Source Archive