:: DESCRIPTION
Repeat enrichment estimator aims to measure the enrichment of annotated repeat types in ChIP-seq data
::DEVELOPER
Peter Park’s lab at CBMI, Harvard Medical School
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Daniel S Day, Lovelace J Luquette, Peter J Park and Peter V Kharchenko.
Estimating enrichment of repetitive elements from high-throughput sequence data.
Genome Biology 2010, 11:R69 doi:10.1186/gb-2010-11-6-r69
:: DESCRIPTION
MICSA (Motif Identification for ChIP-Seq Analysis) is package for the identification of transcription factor binding sites in ChIP-Seq data
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.
Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E.
Nucleic Acids Res. 2010 Jun;38(11):e126. Epub 2010 Apr 7.
:: DESCRIPTION
coMotif is a software of three-component mixture framework to model the joint distribution of two motifs as well as the situation where some sequences contain only one or none of the motifs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Mengyuan Xu, Clarice R. Weinberg, David M. Umbach and Leping Li
coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data
Bioinformatics (2011) 27 (19): 2625-2632.
:: DESCRIPTION
The RSEG software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3. It can work with or without control sample. It can be used to find regions with differential histone modifications patterns, either comparsion between two cell types or between two kinds of histone modifications.
::DEVELOPER
:: SCREENSHOTS
Command
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2011 Mar 15;27(6):870-1. Epub 2011 Feb 16.
Identifying dispersed epigenomic domains from ChIP-Seq data.
Song Q, Smith AD.
:: DESCRIPTION
CASSys (ChIP-seq data Analysis Software System) is an integrated system that supports all steps of computational ChIP-seq data analysis and supersedes the laborious application of several single command line tools. CASSys provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping) and the detection of enriched regions (peakdetection) to various follow-up analyses. The latter are accessible via a state-of-the-art web interface and can be performed interactively by the user. The follow-up analyses allow for flexible user defined association of putative interaction sites with genes, visualization of their genomic context with an integrated genome browser, the detection of putative binding motifs, the identification of over-represented Gene Ontology-terms, pathway analysis and the visualization of interaction networks. The system is client-server based, accessible via a web browser and does not require any software installation on the client side.
::DEVELOPER
Junior Research Group for Application-oriented Bioinformatics, ,Center for Bioinformatics, University of Hamburg
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Alawi, M., Kurtz, S. Beckstette, M. (2011).
CASSys: an integrated software system for the interactive analysis of ChIP-seq data.
Journal of Integrative Bioinformatics, 8(2):155,2011.