Determine if a transcription factor is bound with CENTIPEDE
I wrote a practical tutorial for how to use CENTIPEDE to determine if a transcription factor is bound to a site in the genome. The tutorial explains how to prepare appropriate input data and how to run the analysis. Please get in touch if you have any comments or suggestions. In the future, I would like to incorporate the code from the tutorial into the CENTIPEDE R package.
For details about the statistical models underlying the methods, please see (Pique-Regi, et al. 2011).
The github repository has R code to prepare data for CENTIPEDE. Install and load it like this:
install.packages("devtools") library(devtools) devtools::install_github("slowkow/CENTIPEDE.tutorial") library(CENTIPEDE.tutorial)
After you have installed the code, you can follow along with my commands. Click here to read the tutorial.