Data-driven Network-based Bayesian Inference of Drivers
NetBID (Network-based Bayesian Inference of Drivers) is a data-driven system biology pipeline and toolkit for finding drivers from transcriptomics, proteomics and phosphoproteomics data, where the drivers can be either transcription factors (TF) or signaling factors (SIG).
NetBID 2.0 is an upgraded version of NetBID 1.0 that has been published in Nature in 2018. NetBID 2.0 inherites all the main functions from NetBID 1.0, and provides many more functions and pipelines to perform advanced end-to-end analyses.
Require R >= 3.6.0
. Other dependencies can be found in table https://jyyulab.github.io/NetBID/docs/pre_request.
Installation instructions are in Installation section of the documentation.
Instructions, documentation, and tutorials can be found at:
A PDF manual NetBID_manual.pdf can be found in the repository.
We publish our lastest docker builds on DockerHub. You can pull the docker image by running the following command:
$ docker pull adamdingliang/netbid2:2.0.1
The docker image has build-in RStudio server that can be launched by
$ docker run -it netbid2:2.0.1 rserver --server-daemonize 0
For interactive command line analysis, use the following command:
$ docker run -it netbid2:2.0.1
Demo scripts can be found in demo_scripts directory.
Summary of steps in pipeline_network_demo1.R:
Summary of steps in pipeline_analysis_demo1.R:
Questions that the analyses in analysis_and_plot_demo1.R help to answer:
Part I: More details about the top drivers
Part II: More details about the selected driver
Part III: Other analyses