PhenoGram statistics

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PhenoGram specifications

Information


Unique identifier OMICS_11755
Name PhenoGram
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format text
Output data Images
Output format PNG, JPG, PDF
Programming languages Ruby
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Documentation


Maintainer


  • person_outline Daniel Wolfe <>

Information


Unique identifier OMICS_11755
Name PhenoGram
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format text
Output data Images
Output format PNG, JPG, PDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Ruby
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
RMagick
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

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Documentation


Maintainer


  • person_outline Daniel Wolfe <>

Publication for PhenoGram

PhenoGram in publications

 (8)
PMCID: 5739103
PMID: 28742980
DOI: 10.1080/15592294.2017.1356555

[…] methylated cpg positions to their nearest tsss were calculated with the help of the distancetonearest-function of the “genomicranges” package, and plotted against their corresponding dbvalue., the phenogram shown in the manuscript is a collage of 3 different phenograms (for hypomethylated cpgs, hypermethylated cpgs, and giemsa bands). each phenogram was generated using the web application […]

PMCID: 5591958
PMID: 28928672
DOI: 10.3389/fphys.2017.00648

[…] controls. negative control reactions, with no rna, had undetectable quantification cycle values (cq)., the genetic loci visualization of co-expressed mirnas across chromosomes was performed using phenogram (wolfe et al., ). to determine the significance of the overrepresentation of chromosome regions in the generated co-expressed mirna set, we applied a hypergeometric test., putative mirna […]

PMCID: 5162099
PMID: 27986076
DOI: 10.1186/s12864-016-3377-8

[…] cutoffs of eight for a di-, six for a tri-, and four for tetra-, penta-, and hexanucleotide repeats were used to report ssrs. a maximum distance of 100 bp was allowed between two ssrs. a web based phenogram [] was used to visualize the distribution of the snp loci across the switchgrass pseudomolecules, each line representing a snp locus with its base pair coordinate., supporting data […]

PMCID: 5133618
PMID: 27910910
DOI: 10.1038/srep38260

[…] resulting p-values were corrected using the bonferroni method to accommodate bias due to multiple comparisons., the chromosomal distribution and duplication state of the genes was visualised using phenogram (http://visualization.ritchielab.psu.edu/phenograms/plot - © 2012 ritchie lab). the predicted exon–intron structure was retrieved from the v1 annotation of the grapevine genome […]

PMCID: 4980020
PMID: 27508393
DOI: 10.1371/journal.pone.0160573

[…] the icd-9 categories and descriptions selected through this process, as well as the genes in which the variants are located. this process resulted in 409 associations ()., we used synthesis-view [], phenogram [], and cytoscape [], to visualize the results. synthesis-view was used to visualize the snp-phenotype associations and to plot associations matching previously reported associations […]


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PhenoGram institution(s)
Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Eberly College of Science, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
PhenoGram funding source(s)
This work was supported by the following funding agencies and grants: 5U01 HG004798-03, 5R01 LM010040-02, and U19 HL065962-10.

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