As of August 31st, 2023 the Staphopia API has reached end-of-life
If your research was affected by this shut down, please reach out to Tim Read and/or Robert Petit.
A R library to extract data from the Staphopia API
Tested on R version 3.4
First install the Bioconductor Biostrings and devtools package (if not already installed)
source("https://bioconductor.org/biocLite.R") biocLite("Biostrings") install.packages("devtools") library(devtools)
Install and test staphopia-r from github (running the test might take 1-2 min)
install_github("staphopia/staphopia-r/staphopia") library("staphopia") test_staphopia()
On Mac/ Linux
Create a file in your home directory called ".staphopia" for logging into the API. The file should contain two lines.
TOKEN = "xxxxxxxxxxxxxxxxxxxxxx" USE_DEV = FALSE
For 'TOKEN' substitute the API authenication token string acquired as described above (USE_DEV is a variable for script development and can be ignored)