vignette

A conglomeration of functions that I have written, that I find useful, for analyzing phyloseq objects. Phyloseq objects are a great data-standard for microbiome and gene-expression data.

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

Ubuntu example:

sudo apt install libgdal-dev libudunits2-dev

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

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

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"))

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

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