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Popular tool citations

chevron_left DNA methylation visualization Differentially methylated region detection chevron_right
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EpiExplorer specifications

Information


Unique identifier OMICS_00632
Name EpiExplorer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Publication for EpiExplorer

EpiExplorer in publications

 (18)
PMCID: 5750212
PMID: 29295990
DOI: 10.1038/s41467-017-01586-1

[…] then interrogated for those that were cpg-snps, i.e. where the allelic variation created or abrogated a cpg dinucleotide. 3,873,489 (~31.1%) of these snps were determined to be cpg-snps., we used epiexplorer for our first examination of the hsm peaks for assessment of enrichment for chromatin state (chromhmm), histone modifications and tfbss. we downloaded the additional combined segmentation […]

PMCID: 5727127
PMID: 29234025
DOI: 10.1038/s41467-017-02259-9

[…] browser. the integrative genomics viewer was used for visualization of the data and preparation of browser shots. for annotation of repeats and known chromatin modifications to genomic regions, epiexplorer was used., for sub-nuclear localization studies, setdb1 3td wildtype and mutant domains were cloned in expression constructs containing an nls and fused to mcerulean and mvenus. nih3t3 […]

PMCID: 5613355
PMID: 28946896
DOI: 10.1186/s13072-017-0153-1

[…] using the seqmonk software (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)., the distribution of genes per chromosome, peaks and overlap with chromatin segments was determined with epiexplorer [], and seqminer was used for k-means clustering and heatmap generation []. the spearman correlation of raw data in 10-kb bins and the metagene profiles were generated in deeptools []. […]

PMCID: 5506022
PMID: 28698603
DOI: 10.1038/s41598-017-03434-0

[…] was below 0.001 with a maximum methylation difference of at least 5% and containing at least five cpgs. sig-dmps were annotated using the humanmethylation450 v1.2 manifest file. the freely available epiexplorer tool was used to add further annotation including chromatin state segmentation and histone modifications. enrichment or depletion of sig-dmps in a particular genomic region was determined […]

PMCID: 5522326
PMID: 28467815
DOI: 10.18632/oncotarget.17107

[…] (figure ). more careful investigation of hypermethylated cpg sites revealed that 887 dms were found in cpg islands (cgi). enrichment of wa hypermethylated cpg sites in cgi was also confirmed by the epiexplorer web tool (+28,2% overlapping loci relative to the control set) (figure ) []. of special note, the majority of cpg sites whose methylation increased upon wa treatment in mda-mb-231 cells […]


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