philr
This is the released version of philr; for the devel version, see philr.
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]
Maintainer: Justin Silverman <jsilve24 at gmail.com>
citation("philr")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text |
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 |
See More
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/philr/ |
| Package Short Url | https://bioconductor.org/packages/philr/ |
| Package Downloads Report | Download Stats |