:: DESCRIPTION
MOCCS is a method for for clarifying DNA-binding motif ambiguity.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.
Ozaki H, Iwasaki W.
Comput Biol Chem. 2016 Feb 13. pii: S1476-9271(16)30030-5. doi: 10.1016/j.compbiolchem.2016.01.014.
:: DESCRIPTION
MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genome Biol. 2014;15(10):474.
MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.
Harmanci A1, Rozowsky J, Gerstein M.
:: DESCRIPTION
ChiLin provides a more flexible handle for understanding the ChIP-seq analysis workflow.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2016 Oct 3;17(1):404.
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.
Qin Q, et al.
:: DESCRIPTION
scHMM (correlated hidden Markov models) is a package for analyzing sequence read count data in multiple ChIPseq experiments using sparsely correlated hidden Markov models (HMM).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2013 Mar 1;29(5):533-41. doi: 10.1093/bioinformatics/btt012. Epub 2013 Jan 16.
Sparsely correlated hidden Markov models with application to genome-wide location studies.
Choi H1, Fermin D, Nesvizhskii AI, Ghosh D, Qin ZS.
:: DESCRIPTION
SeqSite was developed for detecting transcription factor binding sites from ChIP-seq data.SeqSite is an efficient and easy-to-use software tool implementing a novel method for identifying and pinpointing transcription factor binding sites. It first detects transcription factor binding regions by clustering tags and statistical hypothesis testing, and locates every binding site in detected binding regions by modeling the tag profiles. It can pinpoint closely spaced adjacent binding sites from ChIP-seq data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Xi Wang and Xuegong Zhang.
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite.
BMC Systems Biology, 5(Suppl 2):S3.
:: DESCRIPTION
peakrots is a bioinformatics analysis tool for optimized ChIP-seq peak detection.
::DEVELOPER
Laura Elo , Aleksi Kallio at CSC — IT Center for Science Ltd
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Methods Mol Biol. 2013;1038:181-91. doi: 10.1007/978-1-62703-514-9_11.
Optimizing Detection of Transcription Factor-Binding Sites in ChIP-seq Experiments.
Kallio A, Elo LL.
:: DESCRIPTION
ChIPmeta is a software for the joint analysis of ChIP-seq and ChIP-chip data. Individual channel-level analysis and joint analysis are performed using hidden Markov models.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
H. Choi, A.I. Nesvizhskii, D. Ghosh, and Z.S. Qin (2009),
Hierarchical HMM with Application to Joint Analysis of ChIP-seq and ChIP-chip Data.
Bioinformatics, 25, 1715-21.
:: DESCRIPTION
ChIPDiff provides a solution for the identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries (L1 and L2). An HMM is employed in ChIPDiff to infer the states of histone modification changes
:: DEVELOPER
Computational & Mathematical Biology Lab @ GIS
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.
Xu H, Wei CL, Lin F, Sung WK.
Bioinformatics. 2008 Oct 15;24(20):2344-9
:: DESCRIPTION
Qeseq is an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mariann Micsinai et al.
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments
Nucl. Acids Res. (2012) 40 (9): e70.
