uc-bd2k / ilincsAPI

ilincsAPI in action

This repository consists of set of examples to showcase the ways of interacting with iLINCS API. The examples in the current folder are implemented in the Jupyter notebook usingIlincsApis.ipynb and "linked" to Google colab.

We also include the same analysis implemented in R markdown -- implemented in the RStudio notebook usingIlincsApis.Rmd and the "knitted" html output of the notebook is provided in usingIlincsApis.html.

Additional R markdown examples are included in subfolders:

• parallelAPI - Using the new parallel API
• useCases - use cases related to the manuscript
• qc - QC code

Get started

To execute the code in the jupyter notebook, please click on the Google colab and execute code "chunks".

R Markdown

See the same example implemented in R Markdown usingIlincsApis.Rmd

The output is included HTML

R Markdown Prerequisites

To execute the code in the useCase notebooks, please install RStudio, launch RStudio and install following R packages: knitr, tinytex, httr, jsonlite, htmltools, data.table and Biobase.

install.packages(c("knitr", "tinytex", "httr", "jsonlite", "htmltools", "data.table"),repos = "http://cran.us.r-project.org")
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager",repos = "http://cran.us.r-project.org");
    
BiocManager::install("Biobase")

Or from shell:

R -e 'install.packages(c("knitr", "tinytex", "httr", "jsonlite", "htmltools","data.table"),repos = "http://cran.us.r-project.org")'
R -e 'if (!require("BiocManager", quietly = TRUE))  install.packages("BiocManager",repos = "http://cran.us.r-project.org"); BiocManager::install("Biobase")'

Render in RStudio

After installing the prerequisites and loading Rmd file into RStudio click on "Knit" to create a HTML/Word output.

Render command line

It is also possible to render the usecases using the command line:

• html output:

R -e 'rmarkdown::render("usingIlincsApis.Rmd", "html_document")'

Execution time

All scripts execute in less than five minutes on a typical desktop or a laptop computer.

For more information about iLINCS and iLINCS API's see links below:

iLINCS API info page

iLINCS API explorer

iLINCS help

iLINCS support group