A Hidden Markov Model for Analyzing ChIP-chip Experiments on Genome Tiling Arrays
A model-based algorithm for finding enriched regions in ChIP-Chip experiments
An integrated webserver for analyzing ChIP-chip data
A intuitive and efficient algorithm for the mapping of millions of query oligonucleotide fragments to the genome of any given length, at least an order of magnitude faster than other popular existing tools
A model-based algorithm for finding enriched regions in ChIP-Seq experiments.
BSMAP is the first general-purpose bisulfite mapping software. It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage.
DyChIPS is designed for comparative analysis of ChIPSeq data whose target sites tend to be broad and are widely distributed across the genome, such as histone modification or some protein binding.
DANPOS is specifically developed for comparison between nucleosome maps generated based on high-throughput sequencing, it detects changes in nucleosome position, occupancy, or fuzziness at single nucleotide resolution.