visPIG - A Web Tool for Producing Multi-Region, Multi-Track, Multi-Scale Plots of Genetic Data
Publication Date
September 10, 2014
Journal
PLOS ONE
Authors
Matthew Scales, Roland Jäger, Gabriele Migliorini, Richard S. Houlston, et al
Volume
9
Issue
9
Pages
e107497
DOI
http://doi.org/10.1371/journal.pone.0107497
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0107497
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25208325
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160258
Europe PMC
http://europepmc.org/abstract/MED/25208325
Web of Science
000342030300085
Scopus
84923324232
Mendeley
http://www.mendeley.com/research/vispig-web-tool-producing-multiregion-multitrack-multiscale-plots-genetic-data
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1669251"], "description"=>"<p>The data tracks plotted across the two regions, 3q26.2 and 8q24.21, are <b>a.</b> association trend test p-values from a CRC GWAS as a colour intensity track, <b>b.</b> significant Hi-C interactions (3 kb resolution; determined from Hi-C experiments on 3 CRC cell-lines, LS174T, LoVo and Colo205), <b>c.</b> ChromHMM functional annotation, <b>d.</b> CRC GWAS trend test association p-values as a SNAP plot (with SNP type (imputed/typed), values and recombination rate). The figure includes a title, gene tracks for both scales and a legend.</p>", "links"=>[], "tags"=>["data types", "Web Tool", "data exploration", "web application", "PNG files", "computer skills", "data visualisation software", "software packages", "visPIG web application", "upload custom data", "Genetic Data", "igv", "ucsc", "custom data uploads", "pdf", "GNU General Public License", "VISual Plotting Interface", "e.g association", "custom features", "web tools"], "article_id"=>1166939, "categories"=>["Biological Sciences"], "users"=>["Matthew Scales", "Roland Jäger", "Gabriele Migliorini", "Richard S. Houlston", "Marc Y. R. Henrion"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0107497.g001", "stats"=>{"downloads"=>4, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Annotated_CRC_GWAS_p_values_for_3q26_2_and_8q24_21_using_data_from_14_and_15_/1166939", "title"=>"Annotated CRC GWAS p-values for 3q26.2 and 8q24.21, using data from [14] and [15].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-10 03:03:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1669252"], "description"=>"<p>This figure shows the same two regions as <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107497#pone-0107497-g001\" target=\"_blank\">Figure 1</a>, 3q26.2 and 8q24.21. The data tracks plotted are the significant 3 kb Hi-C interactions (determined from 3 CRC cell-lines, LS174T, LoVo, Colo205), displayed as arches this time, as well as the corresponding, un-normalised Hi-C reads from the LS174T cell-line as a heat map. Also shown are some manual annotations to highlight the LD block within which one end of the significant interactions have to lie to be plotted, as well as the top CRC risk associated SNP in the LD block, rs6983267.</p>", "links"=>[], "tags"=>["data types", "Web Tool", "data exploration", "web application", "PNG files", "computer skills", "data visualisation software", "software packages", "visPIG web application", "upload custom data", "Genetic Data", "igv", "ucsc", "custom data uploads", "pdf", "GNU General Public License", "VISual Plotting Interface", "e.g association", "custom features", "web tools"], "article_id"=>1166940, "categories"=>["Biological Sciences"], "users"=>["Matthew Scales", "Roland Jäger", "Gabriele Migliorini", "Richard S. Houlston", "Marc Y. R. Henrion"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0107497.g002", "stats"=>{"downloads"=>0, "page_views"=>39, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hi_C_interactomes_of_3q26_2_and_8q24_21_using_data_from_15_/1166940", "title"=>"Hi-C interactomes of 3q26.2 and 8q24.21, using data from [15].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-10 03:03:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1669253"], "description"=>"<p>The comparison has been restricted to the capabilities of visPIG. Some of the other tools have additional features that are not listed here.</p><p>: w = web application, g = locally run graphical user interface, c = locally run from a terminal command line</p><p>: figure output format</p><p>: ability to add a legend onto the output figure</p><p>: v = vector graphics, r = raster graphics</p><p>: possible for some features (e.g. all graphical parameters, the type and order of tracks displayed, the zoom view), but not fully interactive; e.g. to change the plotted regions, the region file needs to be edited and re-uploaded</p><p>: multiple panels can be juxtaposed, which can be used to either show multiple regions and/or zoom in on a specific sub-region; difficult to get different regions on exactly identical scales; we were unable to indicate the location of the zoomed panel on the full view</p><p>: multi-scale in the sense that one can interactively zoom in on a region, but never more than one scale displayed at a given time.</p><p>Comparison of visPIG with other genetic data visualisation tools.</p>", "links"=>[], "tags"=>["data types", "Web Tool", "data exploration", "web application", "PNG files", "computer skills", "data visualisation software", "software packages", "visPIG web application", "upload custom data", "Genetic Data", "igv", "ucsc", "custom data uploads", "pdf", "GNU General Public License", "VISual Plotting Interface", "e.g association", "custom features", "web tools"], "article_id"=>1166941, "categories"=>["Biological Sciences"], "users"=>["Matthew Scales", "Roland Jäger", "Gabriele Migliorini", "Richard S. Houlston", "Marc Y. R. Henrion"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0107497.t001", "stats"=>{"downloads"=>3, "page_views"=>48, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_visPIG_with_other_genetic_data_visualisation_tools_/1166941", "title"=>"Comparison of visPIG with other genetic data visualisation tools.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-09-10 03:03:20"}

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Relative Metric

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