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
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see philr.
Phylogenetic partitioning based ILR transform for metagenomics data
Bioconductor version: 3.4
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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Metagenomics, Microbiome, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (0.5 years) |
| 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_1.0.0.tar.gz |
| Windows Binary | philr_1.0.0.zip |
| Mac OS X 10.9 (Mavericks) | philr_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/philr/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/philr/ |
| Package Downloads Report | Download Stats |
Documentation »
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