philr

This is the released version of philr; for the devel version, see philr.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

Phylogenetic partitioning based ILR transform for metagenomics data

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-5537-637X

Maintainer: Justin Silverman <jsilve24 at gmail.com>

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

Justin Silverman. philr: Phylogenetic partitioning based ILR transform for metagenomics data. doi:10.18129/B9.bioc.philr, R package version 1.38.0, https://bioconductor.org/packages/philr.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version	1.38.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 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

Suggests	testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	mia, miaDash, OMA
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	philr_1.38.0.tar.gz
Windows Binary (x86_64)	philr_1.38.0.zip
macOS Binary (big-sur-x86_64)	philr_1.38.0.tgz
macOS Binary (sonoma-arm64)	philr_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/philr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/philr
Package Short Url	https://bioconductor.org/packages/philr/
Package Downloads Report	Download Stats