philr
This is the development version of philr; for the stable release version, see philr.
Phylogenetic partitioning based ILR transform for metagenomics data
Bioconductor version: Development (3.21)
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:
Maintainer: Justin Silverman <jsilve24 at gmail.com>
citation("philr")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software |
| Version | 1.33.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 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 | |
| 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_1.33.0.tar.gz |
| Windows Binary (x86_64) | philr_1.33.0.zip |
| macOS Binary (x86_64) | philr_1.33.0.tgz |
| macOS Binary (arm64) | |
| 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 |