macro-perfectos-ape-manual

Manual for MACRO-PERFECTOS-APE tools for P-value evaluation, motif comparison and regulatory SNP annotation

https://github.com/vorontsovie/macro-perfectos-ape-manual

Science Score: 18.0%

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Manual for MACRO-PERFECTOS-APE tools for P-value evaluation, motif comparison and regulatory SNP annotation

Basic Info

Host: GitHub
Owner: VorontsovIE
Language: TeX
Default Branch: master
Size: 395 KB

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Created almost 12 years ago · Last pushed about 11 years ago

Metadata Files

Citation

Owner

Name: Ilya Vorontsov
Login: VorontsovIE
Kind: user
Location: Moscow, Russia
Company: VIGG RAS

Website: https://vorontsovie.github.io/about/
Repositories: 36
Profile: https://github.com/VorontsovIE

Programmer, researcher, data analyst and teacher. Doing science (bioinformatics) at VIGG (see @autosome-ru) . Organize "Slon" summer school.

Citation (citations.bib)

@article{MACROAPE,
  title={Jaccard index based similarity measure to compare transcription factor binding site models.},
  author={Vorontsov, Ilya E and Kulakovskiy, Ivan V and Makeev, Vsevolod},
  journal={Algorithms for Molecular Biology},
  volume={8},
  number={1},
  pages={23},
  year={2013}
}


@inproceedings{PERFECTOSAPE,
  title={{PERFECTOS-APE -- Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation.}},
  author={Vorontsov, Ilya E. and Kulakovskiy, Ivan V. and Grigory Khimulya and Nikolaeva, Daria D. and Makeev, Vsevolod J.},
  crossref={Bio:2015},
  pages={102--108}
}
@proceedings{Bio:2015,
  title =        "Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS-2015)",
  booktitle =        "Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS-2015)",
  year =         {2015},
  isbn =         {978-989-758-070-3}
}

@article{Touzet2007,
  title={Efficient and accurate P-value computation for Position Weight Matrices},
  author={Touzet, H{\'e}l{\`e}ne and Varr{\'e}, Jean-St{\'e}phane and others},
  journal={Algorithms Mol Biol},
  volume={2},
  number={1510.1186},
  pages={1748--7188},
  year={2007}
}

@article{Pape2008,
  title={Natural similarity measures between position frequency matrices with an application to clustering},
  author={Pape, Utz J and Rahmann, Sven and Vingron, Martin},
  journal={Bioinformatics},
  volume={24},
  number={3},
  pages={350--357},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{Lifanov2003,
  title={Homotypic regulatory clusters in Drosophila},
  author={Lifanov, Alexander P and Makeev, Vsevolod J and Nazina, Anna G and Papatsenko, Dmitri A},
  journal={Genome research},
  volume={13},
  number={4},
  pages={579--588},
  year={2003},
  publisher={Cold Spring Harbor Lab}
}

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