HPeak - a HMM-based Peak Finder for Next Generation Sequencing Data
Description: HPeak, a HMM-based algorithm for defining read-enriched regions from massive parallel sequencing data
Keywords: next generation sequencing, ChIP-Seq, ChIP-on-Chip, Solexa, computational biology, Hidden markov model, peak identification

## HPeak: A HMM-based algorithm for defining read-enriched regions from massive parallel sequencing data

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History

May 12, 2009: HPeak 2.1

1. Change the counting scheme for minus strand to gain more accuracy on peak location.

Jan. 26, 2009: HPeak 2.0

1. More realistic distributions were used instead of Poisson to model HDF counts in each bin for ChIP-enriched and non-enriched.
2. A new main output file *.hpeak.out is produced to replace .allregions.txt. Additional information was added to this output file: summit--the location within the peak that has the highest HDF coverage) and posterior probability—the normalized cumulative log transformed posterior probability of being ChIP-enriched.
3. Annotation file was fine tuned and more information was added.

Aug. 01, 2008: HPeak 1.1

1. More error checking codes have been added to let Hpeak detect errors timely.
2. Function has been added to report the files names contained in *.inp file in the .sum file.
3. Time display has been changed so it works in windows environment as well.
4. A new sample dataset, sample.stimu_eland-result.txt was added as an example test dataset.
5. Numerous changes have been updated in the manual to make it clear and accurate.

May. 19, 2008: Initial Release.

[ HPeak ] | Qin Lab | Chinnaiyan Lab ]