metilene statistics

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Citations per year

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Popular tool citations

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Associated diseases

Associated diseases


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metilene specifications


Unique identifier OMICS_10901
Name metilene
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input consists of a single SORTED (for genomic positions) tab-separated file.
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.2-4
Stability Stable
Maintained Yes



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  • person_outline Steve Hoffmann <>

Publication for metilene

metilene in pipeline

PMCID: 5786002
PMID: 29374152
DOI: 10.1038/s41467-017-02762-z

[…] a median cpg coverage of ≤4 were excluded from the statistical analysis., for the identification of dmrs between adult heart tissue and cms, we used the binary segmentation algorithm implemented in metilene. for this analysis, we used encode data from human left ventricle and compared it with the merged data obtained from cm nuclei from non-failing adult hearts. a difference of >10 % […]

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metilene in publications

PMCID: 5842653
PMID: 29514626
DOI: 10.1186/s12859-018-2086-5

[…] we show that our approach is superior when compared to dss, a state-of-the-art method for genome-wide differential methylation analysis of wgbs data [, ]. moreover, we provide clear evidence that metilene, a recently proposed method [], cannot be reliably used for identifying aberrant methylation in a test/reference setting, since the statistical framework employed by this method is unable […]

PMCID: 5786002
PMID: 29374152
DOI: 10.1038/s41467-017-02762-z

[…] methylated regions (fmrs) represent genomic regions not overlapping with cpg islands, lmrs, umrs, and pmrs., replicate-based differential methylation analysis (replicate dmr) was performed using metilene for fmrs, cpg islands, lmrs, gumrs, and pmrs. since genic regions downstream of gumrs were frequently partially methylated too, pmrs overlapping a single gene to at least 75% were removed […]

PMCID: 5617875
PMID: 28955039
DOI: 10.1038/s41598-017-12401-8

[…] experiment. it is of interest therefore, to investigate whether the expensive model training can be replaced by computationally more efficient heuristics. this avenue has been explored e.g. in metilene, which uses a fast heuristic to propose differentially methylated regions that are tested for significance only in a second step., in this contribution we describe a general purpose […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] hierarchical model (moabs), hidden markov model (nhmmfdr), three-state hmm (methpipe), shannon entropy (qdmr), and a binary segmentation algorithm combined with a two-dimensional statistical test (metilene). usually, the latest software compares with some previous methods and claims best performance, such as moabs, which can detect the dmrs with a relative low coverage (~10×) and metilene […]

PMCID: 2894748
PMID: 20540800
DOI: 10.1186/1471-2474-11-117

[…] were processed with disectional microscope and cut with ultramicrotome (lkb, stockholm-bromma, sweden). the scar regions were identified on semi-thin sections (for light microscopy) stained with 1% metilene blue, azure ii and basic fuchsin. the el tissue of the lcl was identified on semi-thin sections from the midsubstance in controls and gap region of the transacted ligament for operated […]

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metilene institution(s)
Transcriptome Bioinformatics Group, LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, Leipzig, Germany; RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany; Santa Fe Institute, Santa Fe, New Mexico, USA; Department of Theoretical Chemistry, University of Vienna, Vienna, Austria; Max Planck Institute for Mathematics in Sciences, Leipzig, Germany

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