README.md

In schuyler-smith/phyloschuyler: Functions to help analyze data as phyloseq objects

phylosmith

A supplementary package to build on the phyloseq package. Phyloseq objects are a great data-standard for microbiome and gene-expression data, this package is aimed to provied easy data-wrangling and visualization.

vignette

Installation

Requirements

Linux Systems

For some Linux systems you may need to install the following two programs through your terminal.

Ubuntu example:

sudo apt-get install libmysqlclient-dev libgdal-dev libudunits2-dev libfontconfig1-dev

These programs are required by some dependencies and may not come in your default OS distribution.

Windows Systems

if you are working on WINDOWS you likely need to install the CRAN program Rtools. When prompted, select add rtools to system PATH.

R

phylosmith depends on the usage of the phyloseq package released by Dr. Paul McMurdie. The package is maintained on BioConductor, and can be installed through R using the following commands:

if(!requireNamespace("BiocManager", quietly = TRUE)){
  install.packages("BiocManager")
} 
BiocManager::install("phyloseq")

Additionally, the package imports a number of other packages to use their advanced functions. These packages may install with the phylosmith installation, but it is always best to install independently.

install.packages(c("devtools", "RcppEigen", "RcppParallel", "Rtsne", "ggforce", "units"))

phylosmith

The package is hosted on Github, and can be installed through R with:

remotes::install_github('schuyler-smith/phylosmith')
library(phylosmith)

schuyler-smith/phyloschuyler documentation built on Aug. 16, 2024, 5:36 a.m.