philr

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see philr.

Phylogenetic partitioning based ILR transform for metagenomics data


Bioconductor version: 3.10

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 "3.6") 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

Details

biocViews ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version 1.12.0
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
See More
Suggests testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package philr_1.12.0.tar.gz
Windows Binary philr_1.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) philr_1.12.0.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 3.10 Source Archive