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EpiCompare specifications

Information


Unique identifier OMICS_18813
Name EpiCompare
Interface Web user interface
Restrictions to use None
Output data Identified regions are displayed on a table whose columns are chr, start, end, and link to WashU Epigenome. For Fisher’s exact test and frequency cutoff method, a summary is provided about the distribution of ranks for identified regions. Links are provided to download unmerged 200bp regions or merged regions which merge neighboring 200bp regions. A link to GREAT analysis for merged regions is also provided.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Ting Wang

Information


Unique identifier OMICS_18813
Name EpiCompare
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Ting Wang

Publication for EpiCompare

EpiCompare citations

 (13)
library_books

Genotyping Brucella canis isolates using a highly discriminatory multilocus variable number tandem repeat analysis (MLVA) assay

2017
Sci Rep
PMCID: 5430899
PMID: 28432327
DOI: 10.1038/s41598-017-01114-7

[…] cc, western cape, sourth africa) with permission, and the added pie charts were constructed using bionumerics version 7.6. hunter and gaston discrimination index (hgdi) was calculated using ridom epicompare software version 1.0 (www.ridom.de/epicompare/) to elucidate the discriminatory power of the genotyping methods, which explained the probability of two unrelated and different isolates […]

library_books

Characterization of Multidrug Resistant E. faecalis Strains from Pigs of Local Origin by ADSRRS Fingerprinting and MALDI TOF MS; Evaluation of the Compatibility of Methods Employed for Multidrug Resistance Analysis

2017
PLoS One
PMCID: 5279778
PMID: 28135327
DOI: 10.1371/journal.pone.0171160

[…] to determine the outcome of another method. it also predicts whether the use of any of the methods for determination of the diversity of strains is redundant., all analyses were performed in the epicompare software (ridom bioinformatics, munster, germany), in total, 321 isolates belonging to the genus enterococcus were obtained, with 40% (128 strains) classified as e. faecalis (16s-23s rrna […]

library_books

Utility of Whole Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance

2015
J Clin Microbiol
PMCID: 4609728
PMID: 26354815
DOI: 10.1128/JCM.01066-15

[…] were used to determine the presence of e. coli virulence genes and acquired antibiotic resistance genes with identity thresholds of 85 and 98%, respectively (, )., ridom epicompare (http://www3.ridom.de/epicompare/) was used to calculate the discriminatory power of the typing methods. odds ratios (ors) were calculated with medcalc […]

library_books

Molecular Characterization of Staphylococcus aureus Isolates Transmitted between Patients with Buruli Ulcer

2015
PLoS Negl Trop Dis
PMCID: 4567303
PMID: 26360794
DOI: 10.1371/journal.pntd.0004049

[…] no. ba000018.3] and st8 [col]) was generated using an unweighted-pair group method using average linkages (upgma). the concordance between the two typing methods was calculated with the ridom epicompare software version 1.0 as described previously []., in this study a transmission event is defined to have occurred if the wound of a patient, previously not containing a particular s. aureus […]

library_books

Genetic Diversity of Staphylococcus aureus in Buruli Ulcer

2015
PLoS Negl Trop Dis
PMCID: 4319846
PMID: 25658641
DOI: 10.1371/journal.pntd.0003421

[…] cut-off values (66%, 77%, 79%, 81%, 82% and 84%) were chosen for testing the concordance between mlvf and spa-typing. the concordance between the two dna typing methods was calculated with the ridom epicompare software version 1.0 as described previously []. the cut-off value with the highest concordance between the two typing methods was used for clustering of the mlvf patterns., spa-typing […]

library_books

Analysis of the Population Structure of Anaplasma phagocytophilum Using Multilocus Sequence Typing

2014
PLoS One
PMCID: 3974813
PMID: 24699849
DOI: 10.1371/journal.pone.0093725

[…] (beb) as implemented in codeml was used to identify sites that have evolved under positive selection ., typability, discriminatory indices and wallace coefficients were calculated using ridom epicompare (http://www.ridom.de/epicompare/) and adjusted wallace coefficients using the online tool available at: http://darwin.phyloviz.net/comparingpartitions/index.php?link=tool., in 8 samples […]


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EpiCompare institution(s)
Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
EpiCompare funding source(s)
Supported by the National Institutes of Health [R01HG007354, R01HG007175, R01ES024992, U01CA200060, U24ES026699, U01HG009391] and American Cancer Society Research Scholar [RSG-14-049-01-DMC].

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