venneuler pipeline

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 pipelines

 (3)
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 [53]. fig 3c was generated by taking interactions overlapping promoters (1kb upstream of tss) […]

2017
PMCID: 5611679
PMID: 28979279
DOI: 10.3389/fpls.2017.01614

[…] effectives to a hypergeometric distribution (p-value cut-off = 0.001) using the r “phyper” function. to compare redundancies in the five co-expressed genes lists, a venn diagram was drawn using the venneuler package 1.1 for r., based on the chase domain of the three a. thaliana chks, apple tree genome was browsed to identify putative chk sequences in m. domestica. five candidates […]

2016
PMCID: 4866393
PMID: 27175727
DOI: 10.1186/s12861-016-0111-3

[…] factor target analysis toolkit from webgestalt [27]., to represent the distribution and overlap of transcription factor targets across modules, a venn and euler diagram was generated using the venneuler function supported in r, where areas are proportional to the number of significantly enriched transcription factor targets per module and overlap areas are proportional to the number […]

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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