A R library to extract data from Staphopia's API
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staphopia added option to pull public samples with a location Nov 8, 2017
.gitignore Begin api library for R May 27, 2016
README.md Update README.md Aug 23, 2017

README.md

staphopia-r

A R library to extract data from the Staphopia API

Installation

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")
testthat::test_package("staphopia")

Create user_name and get authenication token

See https://staphopia.emory.edu/docs/api/#authentication

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)

On Windows