eulerAPE protocols

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eulerAPE statistics

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eulerAPE specifications

Information


Unique identifier OMICS_19518
Name eulerAPE
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 3.0.0
Stability Stable
Source code URL http://www.eulerdiagrams.org/eulerAPE/eulerAPE_3.0.0.jar
Maintained Yes

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Maintainer


  • person_outline Luana Micallef <>

Publication for eulerAPE

eulerAPE in pipelines

 (9)
2018
PMCID: 5948225
PMID: 29766023
DOI: 10.1016/j.omtm.2018.02.002

[…] (u6 and h1 promoters, respectively), sequences mapping to these regions were removed from the analysis. circos plots were also employed to visualize aligned reads. venn diagrams were drawn using eulerape. secondary structures of selected reads were visualized by mfold. constraints to force base-pairing of itr regions were used. other parameters were set to default. aggregation plots […]

2017
PMCID: 5465375
PMID: 28580955
DOI: 10.1038/ncomms15677

[…] from wt or ndfip1-deficient etreg or ctreg cells were calculated by log2 fold changes and evaluated for significance using a one-sample t-test. area-proportional venn diagrams were generated with eulerape version 3.0 (http://www.eulerdiagrams.org/eulerape/). the go analysis and corresponding network diagram in was generated with the bingo application in cytoscape. the differentially […]

2017
PMCID: 5499887
PMID: 28541545
DOI: 10.1093/nar/gkx441

[…] program geneious version r7 (). hierarchical clustering and read density plots were generated using easeq (), available from http://easeq.net/. proportional venn diagrams were generated with use of eulerape ()., the new chip-seq and rna-seq data from this publication have been submitted to the gene expression omnibus (geo) and assigned the identifier gse92620., we have recently performed […]

2017
PMCID: 5567995
PMID: 28199302
DOI: 10.1038/nature21372

[…] of transcript per million (fpkm) mapped reads. genes were classified as either meiotic or non-meiotic. the area proportional euler venn diagram for meiotic gene overlap was constructed using eulerape., the microarray and sequencing data that support the findings of this study are available at the ncbi gene expression omnibus (geo) repository under the accession number gse77050. uncropped […]

2017
PMCID: 5668418
PMID: 29097759
DOI: 10.1038/s41598-017-14576-6

[…] query coverage of 50% (qcovhsp), sorted for highest bit-score and lowest e-value and removed multiple identical top hits after manual inspection as not informative in the context of rbh. we used eulerape v.3.0.0 to draw area-proportional venn diagrams to visualize the overlap among gene sets., third, we tested if metagenome-based assemblies are reliable to study fungal gene space […]


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eulerAPE in publications

 (47)
PMCID: 5955448
PMID: 29532717
DOI: 10.1080/21505594.2018.1449508

[…] all these microarrays were performed using gpl200 platform (affimetrix). all comparisons were performed between upregulated genes only. area-proportional venn diagrams were drawn using the eulerape (http://www.eulerdiagrams.org/eulerape/v2/)., statistical significance of overlaps between microarray conditions was determined based on hypergeometric probability., the coding sequence […]

PMCID: 5823883
PMID: 29472578
DOI: 10.1038/s41467-018-03091-5

[…] with the exception of venom obtained by harassment, where three insects were used due to the lower amount of venom available. the area-proportional venn diagram shown in figure 2b was produced using eulerape software []., nucleotide and protein sequences discovered in this project were submitted to genbank and assigned the accession numbers ky030911–ky031319. raw sequencing reads […]

PMCID: 5948225
PMID: 29766023
DOI: 10.1016/j.omtm.2018.02.002

[…] (u6 and h1 promoters, respectively), sequences mapping to these regions were removed from the analysis. circos plots were also employed to visualize aligned reads. venn diagrams were drawn using eulerape. secondary structures of selected reads were visualized by mfold. constraints to force base-pairing of itr regions were used. other parameters were set to default. aggregation plots […]

PMCID: 5797619
PMID: 29441081
DOI: 10.3389/fpls.2018.00049

[…] in the hybrid, four pairwise comparisons were done: t3-8 vs. b.g. tritici, t3-8 vs. b.g. secalis, thun-12 vs. b.g. tritici and thun-12 vs. b.g. secalis. the venn diagramms were produced using eulerape (micallef and rodgers, )., we have also compared our mapping and read count strategy with the rna-seq analysis pipeline “salmon” (patro et al., ), using standard parameters. correlation […]

PMCID: 5765030
PMID: 29323144
DOI: 10.1038/s41598-017-18699-8

[…] and if they agree with the set inclusion criteria will be added to our access and sql databases and will be visible on our website., the venn diagrams used to analyse these data were produced using eulerape., in order to characterise the functionality of msp, bliss and paxdb we uploaded the gene list of each proteome into qiagen’s ingenuity pathway analysis (ipa, qiagen redwood city, […]


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eulerAPE institution(s)
School of Computing, University of Kent, Canterbury, CT, USA

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