Difference between revisions of "Diffreps"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=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. | |sw summary=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. | ||
| − | |bio domain=ChIP- | + | |bio domain=ChIP-seq, |
| − | |bio method= | + | |bio method=Differential Binding, |
|bio tech=Illumina, ABI SOLiD, | |bio tech=Illumina, ABI SOLiD, | ||
|created by=Li SHEN | |created by=Li SHEN | ||
Latest revision as of 10:18, 11 January 2016
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Application data |
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| Created by | Li SHEN |
|---|---|
| Biological application domain(s) | ChIP-seq |
| Principal bioinformatics method(s) | Differential Binding |
| Technology | Illumina, ABI SOLiD |
| Created at | The Mount Sinai School of Medicine |
| Maintained? | Yes |
| Input format(s) | bed |
| Output format(s) | differential sites/peaks |
| Software features | Multiple replicates information used; automated pipeline; easy genomic annotation; finding hotspots; |
| Programming language(s) | Perl |
| Licence | GPLv3 |
| Operating system(s) | Linux, Windows, Mac OS X |
Summary: 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.
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Description
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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