- Model-based Analysis of Tiling-array (MAT)
A model-based algorithm for finding enriched regions in ChIP-Chip experiments.
- Cis-regulatory Element Annotation System (CEAS)
An integrated webserver for analyzing ChIP-chip data.
- extreme MApping of OligoNucleotides (xMAN)
A simple and efficient method for the mapping of millions of query oligonucleotide fragments to the subject genome of any given length, at least an order of magnitude faster than other popular existing tools.
- Model-based Analysis of ChIP-sequencing (MACS)