To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("philr")

In most cases, you don't need to download the package archive at all.

philr

 

Phylogenetic partitioning based ILR transform for metagenomics data

Bioconductor version: Release (3.5)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("philr")

Documentation

HTML R Script Introduction to PhILR
PDF   Reference Manual
Text   NEWS

Details

biocViews Metagenomics, Microbiome, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
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
Build Report  

Package Archives

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

Package Source philr_1.2.0.tar.gz
Windows Binary philr_1.2.0.zip
Mac OS X 10.11 (El Capitan) philr_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/philr/tree/release-3.5
Package Short Url http://bioconductor.org/packages/philr/
Package Downloads Report Download Stats

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