:: DESCRIPTION
BroadPeak is an algorithm for the identification of broad peaks from diffuse ChIP-seq datasets.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Feb 15;29(4):492-3. doi: 10.1093/bioinformatics/bts722. Epub 2013 Jan 7.
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
Wang J, Lunyak VV, Jordan IK.
:: DESCRIPTION
MOSAICS is an R package for the analysis of one-sample or two-sample ChIP-seq data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kuan, P., Chung, D., Pan, G., Thomson, J., Stewart, R., and Keles, S. (2011).
A Statistical Framework for the Analysis of ChIP-Seq Data.
Journal of the American Statistical Association
:: DESCRIPTION
NucHunter is an algorithm that uses the data from ChIP-seq experiments directed against many histone modifications to infer positioned nucleosomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Oct 15;29(20):2547-54. doi: 10.1093/bioinformatics/btt449. Epub 2013 Aug 26.
Inferring nucleosome positions with their histone mark annotation from ChIP data.
Mammana A1, Vingron M, Chung HR.
:: DESCRIPTION
cnvCSEM (CNV: -guided C: hIP-S: eq by E: xpectation-M: aximization algorithm), is a flexible framework that incorporates CNV in multi-read allocation.
::DEVELOPER
Qi Zhang (qizhang at stat dot wisc dot edu)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
CNV-guided Multi-read Allocation for ChIP-seq.
Zhang Q, Keleş S.
Bioinformatics. 2014 Jun 24. pii: btu402.
:: DESCRIPTION
Sole-Search is an integrated peak-calling and analysis softwar which is available through a user-friendly interface and (i) converts raw data into a format for visualization on a genome browser, (ii) outputs ranked peak locations using a statistically based method that overcomes the significant problem of false positives, (iii) identifies the gene nearest to each peak, (iv) classifies the location of each peak relative to gene structure, (v) provides information such as the number of binding sites per chromosome and per gene and (vi) allows the user to determine overlap between two different experiments.
::DEVELOPER
Korf Lab at the University of California, Davis.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2010 Jan;38(3):e13. doi: 10.1093/nar/gkp1012. Epub 2009 Nov 11.
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.
Blahnik KR, Dou L, O’Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Lud?scher B, Korf I, Farnham PJ.
:: DESCRIPTION
CHANCE (ChIP-seq Analytics and Confidence Estimation) is a software for assessing the quality of ChIP-seq experiments and providing feedback for the optimization of ChIP and library generation protocols.
CHANCE-HT is a ChIP-seq pre-processing software that filters samples with weak IP-strength, identifies heavily biased control experiments and under sequenced samples, detects batch effects, and normalizes large ensembles of ChIP-seq datasets.CHANCE-HT uses a parallel processing approach to normalize and filter large collections of ChIP-seq datasets in tandem.
::DEVELOPER
Diaz Lab , Jun S. Song’s Research Group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
A. Diaz, A. Nellore, J.S. Song.
CHANCE: a comprehensive software for quality control and validation of ChIP-seq data,
Genome Biology 13:R98, (2012).
:: DESCRIPTION
CSDeconv maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach
::DEVELOPER
:: SCREENSHOTS
N/a
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
D. S. Lun, A. Sherrid, B. Weiner, D. R. Sherman, and J. E. Galagan.
A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-Seq data.
Genome Biol., 10(12):R142, December 2009.
:: DESCRIPTION
ODIN is a HMM-based approach to detect and analyse differential peaks in pairs of ChIP-seq data. It is the first differential peak caller that performs genomic signal processing, peak calling and p-value calculation in an integrated framework.
::DEVELOPER
IZKF Computational Biology and Bioinformatics Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Detecting differential peaks in ChIP-seq signals with ODIN.
Allhoff M, Seré K, Chauvistré H, Lin Q, Zenke M, Costa IG.
Bioinformatics. 2014 Nov 3. pii: btu722.
:: DESCRIPTION
ReMap is an integrative analysis of transcription factor ChIP-seq experiments
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Cheneby J., Menetrier Z., Mestdagh M., Rosnet T., Douida A., Rhalloussi W., Bergon A., Lopez F., Ballester B.
ReMap 2020: A database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments.
Nucleic Acids Research (2020) gkz945 https://doi.org/10.1093/nar/gkz945.
Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape.
Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B.
Nucleic Acids Res. 2015 Feb 27;43(4):e27. doi: 10.1093/nar/gku1280.
:: DESCRIPTION
Given a set of peaks from (biological or technical) replicates, MSPC combines the p-values of overlapping enriched regions: users can choose a threshold on the combined significance of overlapping peaks and set a minimum number of replicates where the overlapping peaks should be present. The method allows the “rescue” of weak peaks occuring in more than one replicate and outputs a new set of enriched regions for each replicate.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Using combined evidence from replicates to evaluate ChIP-seq peaks.
Jalili V, Matteucci M, Masseroli M, Morelli MJ.
Bioinformatics. 2015 May 7. pii: btv293.
