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Short description:
Please summarise the application in a few sentences. Avoid links here. diffReps is developed to find different peaks in ChIP-seq. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. diffReps takes into account the biological variations within a group of samples and uses that information to enhance the statistical power. Considering biological variation is of high importance, especiallly for in vivo brain tissues.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
ChIP-seq,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Differential Binding,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Illumina, ABI SOLiD,
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
The Mount Sinai School of Medicine
== Description == <!-- Describe the application in the space below --> ChIP-seq is now widely used to profile the enrichment of a DNA-binding protein on a genome. It is of high interest to compare the binding differences of a histone mark or transcription factor between two contrasting conditions, such as disease vs. control. diffReps is developed to serve this purpose. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. diffReps takes into account the biological variations within a group of samples and uses that information to enhance the statistical power. Considering biological variation is of high importance, especiallly for in vivo brain tissues (which is my group's high priority). <!-- -->
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