useCases

iLincs API useCases

Prerequisites

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

install.packages(c("knitr", "tinytex", "httr", "jsonlite", "htmltools", "httr", "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(c("Biobase", "ComplexHeatmap", "enrichR"))

Or from shell:

R -e 'install.packages(c("knitr", "tinytex", "httr", "jsonlite", "htmltools", "httr", "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(c("Biobase", "ComplexHeatmap", "enrichR"))'

Use Cases

	R Markdown source	PDF/HTML output	Web walkthrough
► useCase1a Identifying chemical perturbagens emulating genetic perturbation of MTOR protein	useCase1a.Rmd	PDF / HTML	link
► useCase1b Mechanism of action analysis via connection to genetic perturbation signatures	useCase1b.Rmd	PDF / HTML	link
► useCase2 Proteo-genomics analysis of cancer driver events in breast cancer	useCase2.Rmd	PDF / HTML	link

Creating Output

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

Render command line

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

• html output:

R -e 'rmarkdown::render("useCase1a.Rmd", "html_document")'

• pdf output:

R -e 'rmarkdown::render("useCase1a.Rmd", "pdf_document")'