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TCIApathfinder

Travis build status

TCIApathfinder is a wrapper for The Cancer Imaging Archive’s REST API v3. The Cancer Imaging Archive (TCIA) hosts de-identified medical images of cancer available for public download, as well as rich metadata for each image series. TCIA provides a REST API for programmatic access to the data. This package provides simple functions to access each API endpoint. For more information about TCIA, see TCIA’s website.

TCIApathfinder is on CRAN.

Installation

From within R:

install.packages("TCIApathfinder")

From GitHub:

# install.packages("devtools")
devtools::install_github("pamelarussell/TCIApathfinder")

Authentication

An API key is not needed to access public collections on TCIA but it could be useful for private collections. To obtain and correctly store your API key:

  1. Request a key from TCIA by following the instructions here.

  2. Create a text file in your home directory (~/) called .Renviron.

  3. Create the contents of the .Renviron file like this, making sure the last line in the file is empty. Otherwise, R will silently fail to load the file.

    TCIA_API_KEY=xxx-xxx-xxx-xxx

  4. Restart R. .Renviron is only processed at the beginning of an R session.

Package usage

Detailed vignettes on package usage and downstream image analysis can be viewed on CRAN or from within an R session with browseVignettes("TCIApathfinder").

Citation

From within R:

citation("TCIApathfinder")

TCIApathfinder: An R Client for the Cancer Imaging Archive REST API. Pamela Russell, Kelly Fountain, Dulcy Wolverton and Debashis Ghosh. Cancer Res August 1 2018 (78) (15) 4424-4426; DOI: 10.1158/0008-5472.CAN-18-0678.

More information on the TCIA REST API

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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