Skip to content

Latest commit

 

History

History
84 lines (55 loc) · 3.3 KB

README.md

File metadata and controls

84 lines (55 loc) · 3.3 KB
Raw

ImmPortR

R-CMD-check Coverage status Lifecycle: maturing

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.

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

Register and set ImmPort credentials

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")