Benchmarking Study of Covariate-Adjusted FDR Methods

This repository includes all code used to perform analyses and generate figures for the manuscript, A practical guide to methods controlling false discoveries in computational biology.

Notes

Before attempting to run the code in this repository, please read the following notes.

Cloning

We do not recommond cloning this entire repository. The repository includes all historical commits and is incredibly large. Instead, we recommend either making a shallow clone of the repository using the following code.

 git clone --depth=1 https://github.com/pkimes/benchmark-fdr.git

SummarizedBenchmark

The code in this repository was run using an older version of the SummarizedBenchmark package and will not run with newer versions of the package. An older version of the package should be installed from GitHub using the following R code.

devtools::install_github("areyesq89/SummarizedBenchmark", ref = "fdrbenchmark")

Rendered reports

Final rendered Rmd files for simulations and case studies included in the manuscripts are available in this repository, and are rendered here via GitHub pages.

Citation

Korthauer K†, Kimes PK†, Duvallet C‡, Reyes A‡, Subramanian A‡, Teng M, Shukla C, Alm EJ, Hicks SC*. A practical guide to methods controlling false discoveries in computational biology. bioRxiv. doi: https://doi.org/10.1101/458786

†: co-first authors, ‡: co-second authors, *: corresponding author

License/Copyright

All code in this project is made available under a MIT license.
All non-code text in this project is made available under a CC BY-NC-ND 4.0 license.