T-KDE is a software tool that can be used to locate constitutive protein binding sites using ChIP-seq peak centers from multiple cell lines or genomic “hot spots” where several different proteins bind and, conversely, cell-specific sites bound by a given protein. T-KDE combines a binary range tree algorithm, a non-parametric kernel density estimator, and a mode finding algorithm.
The Matlab source code, examples, a shell script and a readme file can be downloaded below. Note that the current version of the package has not been tested on a 32-bit machine.
Download the software for T-KDE (15MB) .
Leping Li, Ph.D.