ImmPortR

ImmPortR is an R wrapper around the ImmPort API to query datasets from ImmPort Shared Data and upload data to ImmPort Private Data, and it also utilizes the Aspera CLI to download files from ImmPort Shared Data.

What is ImmPort?

ImmPort is funded by the NIH, NIAID and DAIT in support of the NIH mission to share data with the public. Data shared through ImmPort has been provided by NIH-funded programs, other research organizations and individual scientists ensuring these discoveries will be the foundation of future research.

Installation

ImmPortR

# install.packages("remotes")
remotes::install_github("RGLab/ImmPortR")

The Aspera CLI

The IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.

• Download
• Documentation

Take a look at this for guidance on installing the Aspera CLI.

Register and set ImmPort credentials

• Register
• Read the User Agreement for ImmPort
• Set environment variables with your ImmPort credentials, on your R console:

Sys.setenv(ImmPortUsername = "yourImmPortUsername")
Sys.setenv(ImmPortPassword = "yourImmPortPassword")

• Or in .Renviron file in your home directory:

ImmPortUsername=yourImmPortUsername
ImmPortPassword=yourImmPortPassword

Usage

Query datasets

library(ImmPortR)

elisa <- query_dataset("SDY269", "elisa")
elispot <- query_dataset("SDY269", "elispot")
fcsAnalyzed <- query_dataset("SDY269", "fcsAnalyzed")
hai <- query_dataset("SDY269", "hai")
hlaTyping <- query_dataset("SDY269", "hlaTyping")
kirTyping <- query_dataset("SDY269", "kirTyping")
mbaa <- query_dataset("SDY269", "mbaa")
neutAbTiter <- query_dataset("SDY269", "neutAbTiter")
pcr <- query_dataset("SDY269", "pcr")

Download files

download_immport("/SDY1/StudyFiles/Casale_Study_Summary_Report.doc")

Validate data

validate_zip("yourStudyData.zip", workspace_id = 99999, upload_notes = "for SDY9999")