venneuler protocols

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venneuler specifications

Information


Unique identifier OMICS_19412
Name venneuler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.1-0
Stability Stable
Requirements
rJava
Source code URL https://cran.r-project.org/src/contrib/venneuler_1.1-0.tar.gz
Maintained Yes

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Maintainer


  • person_outline Leland Wilkinson <>

Publication for venneuler

venneuler in pipeline

2017
PMCID: 5438180
PMID: 28475589
DOI: 10.1371/journal.pgen.1006749

[…] harvested, isolated, rrna-depleted, and sequenced in parallel to the ago4 dataset. overlaps in differential expression were calculated from edger and plotted as a weighted venn diagram using the venneuler package in r., dap-seq transcription factor binding sites came from the geo accession gse60141 []. was generated by taking interactions overlapping promoters (1kb upstream of tss) on one […]


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venneuler in publications

 (30)
PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] generate values for plotting venn diagrams and associated bed files for further analysis. only literal overlaps (overlapping by 1 bp) were considered. venn diagrams were plotted using the r package ‘venneuler’ (https://cran.rproject.org/web/packages/venneuler/index.html)., to calculate the distance of consensus peaks from tsss and gc percentage of accessible regions, the homer (v3.12) command […]

PMCID: 5934840
PMID: 29755730
DOI: 10.1186/s13601-018-0201-3

[…] diagram was used to quantify the proportion of individuals with different asthma phenotypes and to illustrate the overlap., the diagrams were created using r software version 3.2.0 (“venndiagram”, “venneuler” and “reshape2” packages) and all statistical analyses were performed in stata version 13.1 (statacorp, tx, usa), using the survey command to account for the complex sampling design […]

PMCID: 5726629
PMID: 29232382
DOI: 10.1371/journal.pone.0189084

[…] transcription factor and canonical pathway gene set enrichment analysis was performed using r statistical programming language []. r packages utilized include colormap [], gplots [], openxlsx [] and venneuler []., circos plots were generated from command line using the tableviewer plugin. following integration of the transcription factor and canonical pathway/hallmark test results data […]

PMCID: 5681658
PMID: 29127421
DOI: 10.1038/s41598-017-15220-z

[…] with 999 permutations on beta-diversity values using vegan package. the number of identical otus between skin microbiota and planktonic communities was analyzed using an euler diagramm computed with venneuler r-package. to assess how each microbial clade contributed to the dissimilarity between planktonic and skin microbiotas, as well as between microbiotas of cetacean species, we performed […]

PMCID: 5438180
PMID: 28475589
DOI: 10.1371/journal.pgen.1006749

[…] harvested, isolated, rrna-depleted, and sequenced in parallel to the ago4 dataset. overlaps in differential expression were calculated from edger and plotted as a weighted venn diagram using the venneuler package in r., dap-seq transcription factor binding sites came from the geo accession gse60141 []. was generated by taking interactions overlapping promoters (1kb upstream of tss) on one […]


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venneuler institution(s)
Systat Software Inc., San Jose, CA, USA; Northwestern University, Evanston, IL, USA; Computer Science, University of Illinois, Chicago, IL, USA
venneuler funding source(s)
Supported by NSF/DHS grant DMS-FODAVA-0808860.

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