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Protocols

Epiviz specifications

Information


Unique identifier OMICS_12439
Name Epiviz
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 4.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Hector Corrada Bravo

Information


Unique identifier OMICS_12439
Name Epiviz
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.10.0
Stability Stable
Requirements
methods
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Hector Corrada Bravo

Publications for Epiviz

Epiviz citations

 (5)
library_books

Enhanced JBrowse plugins for epigenomics data visualization

2018
BMC Bioinformatics
PMCID: 5921565
PMID: 29699480
DOI: 10.1186/s12859-018-2160-z

[…] aphical tools such as genome browsers are able to properly visualize these specialized data sets. Current genome browsers such as UCSC genome browser [], AnnoJ [], IGV [], WashU EpiGenome Browser [], Epiviz [], IGB [], and JBrowse [], have limited capability to visualize these data sets effectively, hindering the visualization and potential discoveries with new sequencing technologies. JBrowse is […]

call_split

Metaviz: interactive statistical and visual analysis of metagenomic data

2018
Nucleic Acids Res
PMCID: 5887897
PMID: 29529268
DOI: 10.1093/nar/gky136
call_split See protocol

[…] ata visualization. Given the structure of metagenomic data, the user navigation tools and the database storage are tailored to taxonomic hierarchies. We moved from a relational database model used in Epiviz (), our previous interactive data analysis tool for functional genomic data such as gene expression and methylation data, to a graph database to manage the feature hierarchy and abundance count […]

library_books

C State: an interactive web app for simultaneous multi gene visualization and comparative epigenetic pattern search

2017
BMC Bioinformatics
PMCID: 5606219
PMID: 28929968
DOI: 10.1186/s12859-017-1786-6

[…] AVIS [], which links to the UCSC browser and uses a chromosome-centric approach. Complete ChIP-seq analysis packages like CisGenome [] and recently developed visualization tools such as VisPIG [] and Epiviz [] offer options for peak visualization but cannot directly screen and display user-defined patterns across multiple loci. Another challenge faced by biologists is that many of the current tool […]

call_split

Visual analytics of geo social interaction patterns for epidemic control

2016
PMCID: 4980799
PMID: 27510908
DOI: 10.1186/s12942-016-0059-3
call_split See protocol

[…] ameters in the Table . The tool can be applied to study other emerging infectious diseases (e.g., measles) directly with the input of their corresponding parameters.In terms of control strategies, GS-EpiViz allows users to design four vaccination strategies: random-based, degree-based, betweenness-based, and strength-based vaccination strategies; these are selected because they are the most typica […]

library_books

Public data and open source tools for multi assay genomic investigation of disease

2015
Brief Bioinform
PMCID: 4945830
PMID: 26463000
DOI: 10.1093/bib/bbv080

[…] y enables inspection of specific cancer genomic loci or the general overview of genomic alterations, the exploration of cause–effect relationships between various alteration types. Most recently, the Epiviz genome browser [] provides both a web-based interface and full integration with Bioconductor and its core data classes through the ‘Epivizr' package. Visualization tools tied to genomic coordin […]

Citations

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Epiviz institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA; University of Maryland Institute of Advanced Computer Studies, University of Maryland, College Park, College Park, MD, USA; Department of Computer Science, University of Maryland, College Park, College Park, MD, USA
Epiviz funding source(s)
Supported by the grant funded by the National Institutes of Health [R01GM114267].

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