This repository contains the software implementations for INTRIGUE, a statistical method to quantify and control reproducibility in high-throughput experiments. The statistical models and the computational procedures are described in [1].
The repository includes source code (C/C++ and R) and necessary data/scripts to replicate all the analysis results described in [1]. A docker image that replicate the original computational environment for the analysis is also included.
Software distributed under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. See LICENSE for more details.
The computational methods are implemented in R and C/C++.
Source code for R package INTRIGUE is included in R_src. To install, run
library(devtools)
install_github("ArtemisZhao/INTRIGUE/R_src")
The pdf manual for the R package is available in here.
C/C++ code for a standalone binary executable is in cpp_src. To compile, run
make
The command line options for running the binary are described in here.
The necessary code and data for simulation and real data application described in the INTRIGUE paper are included in intrigue_paper. They should enable readers to fully reproduce our results.
We provide a docker image to reproduce all our analysis described in the INTRIGUE paper. The detailed instructions are available in docker directory.
- Yi Zhao (University of Michigan)
- Xiaoquan Wen (Univerisity of Michigan)
[1] INTRIGUE: Quantify and Control Reproducibility in High-throughput Experiments. Zhao, Y., Sampson, M., and Wen, X. (2020) [preprint]