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philr

Phylogenetic partitioning based ILR transform for metagenomics data


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends
Imports ape, phangorn, tidyr, ggplot2, ggtree, methods
System Requirements
URL https://github.com/jsilve24/philr
Bug Reports https://github.com/jsilve24/philr/issues
See More
Suggests testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia
Linking To
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Build Report Build Report

Package Archives

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

Source Package philr_1.28.0.tar.gz
Windows Binary philr_1.28.0.zip
macOS Binary (x86_64) philr_1.28.0.tgz
macOS Binary (arm64) philr_1.28.0.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