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GSA-BenchmarKING

(A repository of workflows and shiny apps for GSA methods benchmarking)

GMU

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.


Comments? Bugs?

Contact us at: thegsacentral at gmail.

GMU

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

GMU

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:

"ss-shiny" is a Shiny app for some of the existing single-sample GSA tools. Open R and run ss-shiny in two simple steps:

Install required packages
Run app

gr-shiny:

"gr-shiny" is a Shiny app for some of the existing genomic-range GSA tools. Open R and run gr-shiny in two simple steps:

Install required packages
Run app

Notes on testing:
Reported successful and unsuccessful testing configurations

GSA Central, 2020

Last updated: Jun 30th, 2020