GSA-BenchmarKING

Welcome!

GSA-BenchmarKING is a repository of apps/workflows/pipelines that allow benchmarking GSA software in an easy and automated way. Currently, GSA-BenchmarKING contains jupyter notebooks with full workflows for benchmarking GSA methods, and shiny apps that allow benchmarking with the click of a few buttons.

For Authors

If you want to contribute with a notebook or app to benchmark a given set of GSA methods, please contact us at: thegsacentral at gmail.

Benchmarking workflows:

In the following workflows, you can follow a GSA benchmark process from the source data to the results.

Single-sample GSA workflows:

Download
Open

Genomic-region GSA workflows:

Download
Open

Benchmarking Apps:

The following apps allow the user to perform benchmark of specific GSA methods, but also to introduce their own gold standard dataset, select comparison metrics, and other advantages.

ss-shiny (benchmarking single-sample GSA methods)

gr-shiny (benchmarking genomic-region GSA methods)

Notes on testing:

(Please note that loading of the shiny apps might take several minutes)
Reported successful and unsuccessful testing configurations