StereoGene specifications

Information


Unique identifier OMICS_19661
Name StereoGene
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some genomic annotations.
Input format BED, WIG, BedGraph, BroadPeak
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.73
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline favorov
  • person_outline Elena Stavrovskaya

Publication for StereoGene

StereoGene citation

library_books

Epigenetic regulation of gene expression in cancer: techniques, resources and analysis

2017
Brief Funct Genomics
PMCID: 5860551
PMID: 28968850
DOI: 10.1093/bfgp/elx018

[…] y divided into: (1) linear models comparing peaks similar to DMRs, such as DiffBind []; (2) hidden Markov models (HMMs), such as ChiPDiff [] and ChromHMM []; or (3) whole-genome correlations, such as StereoGene [] and GenometriCorr []. For all data platforms, more advanced methods using mixture models, Shannon entropy, logistic regression, nonnegative matrix factorization, clustering, feature sele […]

StereoGene institution(s)
Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia; Institute for Information Transmission Problems, RAS, Moscow, Russia; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russia; Laboratory of Bioinformatics, Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia
StereoGene funding source(s)
Supported by Russian Science Foundation (grant 14- 24-00155), by National Institutes of Health (grants P30 CA006973 and NCI R01CA177669), by Allegheny Health Network-Johns Hopkins Cancer Research Fund and JHU IDIES/Moore Foundation and by Russian Foundation for Basic Research (grants 14-04-01872 and 14-04-00576).

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