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diChIPMunk specifications
Information
Unique identifier | OMICS_00481 |
---|---|
Name | diChIPMunk |
Software type | Package/Module |
Interface | Command line interface |
Restrictions to use | None |
Input data | A DNA sequence |
Output data | DiChIPMunk converts all DNA sequences from mono to dinucleotide alphabet. Each dinucleotide is constructed from two single neighboring nucleotide letters. |
Operating system | Unix/Linux |
Programming languages | Java |
Computer skills | Advanced |
Version | 4.3 |
Stability | Stable |
Maintained | Yes |
Versioning
No version available
Documentation
Maintainer
- person_outline Ivan Kulakovskiy
Publication for diChIPMunk
From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites.
diChIPMunk citations
(4)Combining phylogenetic footprinting with motif models incorporating intra motif dependencies
[…] ndencies have been shown to outperform simpler motif models like the PWM model [–]. Examples for highly popular tools that model intra-motif dependencies are Dimont [], MEME-ChIP [], DeepBind [], and diChIPMunk [].In contrast, the second group of de-novo motif discovery approaches known as phylogenetic footprinting incorporates orthologous sequences of at least two phylogenetically related species […]
Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long range interactions in Drosophila
[…] as done using MACS2 () (https://github.com/taoliu/MACS) against preimmune and input control data. Peak sets obtained with the preimmune control were smaller and were utilized for motif discovery with diChIPMunk (,). Resulting dinucleotide position weight matrices were used for motif finding in peaks obtained with the input control. To detect peaks with strong motif occurrences, we estimated a P-va […]
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP Seq data
[…] e of pattern matching and pattern detection approaches for TFBS prediction in the context of ChIP-Seq data, we applied oPWM and SiteGA (as representatives of the former class) as well as ChIPMunk and diChIPMunk (as representatives of the latter class) to analyze a dataset of 4455 FoxA2-binding loci (ChIP-Seq peaks with read coverage of at least 15) in mouse adult liver chromatin [].To produce a su […]
A general approach for discriminative de novo motif discovery from high throughput data
[…] otif order 1 than for motif order 0 for at least one combination of training and test data sets in Supplementary Figure S5–S13, and we compare the dependencies detected by Dimont to those detected by diChIPMunk () in Section 6 of the Supplementary Material. […]
Citations
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