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{"title"=>"VisPIG - A web tool for producing multi-region, multi-track, multi-scale plots of genetic data", "type"=>"journal", "authors"=>[{"first_name"=>"Matthew", "last_name"=>"Scales", "scopus_author_id"=>"56979891400"}, {"first_name"=>"Roland", "last_name"=>"Jäger", "scopus_author_id"=>"26321678200"}, {"first_name"=>"Gabriele", "last_name"=>"Migliorini", "scopus_author_id"=>"55819409200"}, {"first_name"=>"Richard S.", "last_name"=>"Houlston", "scopus_author_id"=>"34569730700"}, {"first_name"=>"Marc Y.R.", "last_name"=>"Henrion", "scopus_author_id"=>"55224880200"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"608759134", "sgr"=>"84923324232", "doi"=>"10.1371/journal.pone.0107497", "scopus"=>"2-s2.0-84923324232", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"25208325"}, "id"=>"88097ec2-2278-3f4b-a337-01d4d1ab1336", "abstract"=>"We present VISual Plotting Interface for Genetics (visPIG; http://vispig.icr.ac.uk), a web application to produce multi-track, multi-scale, multi-region plots of genetic data. visPIG has been designed to allow users not well versed with mathematical software packages and/or programming languages such as R [1], Matlab®, Python, etc., to integrate data from multiple sources for interpretation and to easily create publication-ready figures. While web tools such as the UCSC Genome Browser [2] or the WashU Epigenome Browser [3] allow custom data uploads, such tools are primarily designed for data exploration. This is also true for the desktop-run Integrative Genomics Viewer (IGV) [4],[5]. Other locally run data visualisation software such as Circos [6] require significant computer skills of the user. The visPIG web application is a menu-based interface that allows users to upload custom data tracks and set track-specific parameters. Figures can be downloaded as PDF or PNG files. For sensitive data, the underlying R [1] code can also be downloaded and run locally. visPIG is multi-track: it can display many different data types (e.g association, functional annotation, intensity, interaction, heat map data,…). It also allows annotation of genes and other custom features in the plotted region(s). Data tracks can be plotted individually or on a single figure. visPIG is multi-region: it supports plotting multiple regions, be they kilo- or megabases apart or even on different chromosomes. Finally, visPIG is multi-scale: a sub-region of particular interest can be 'zoomed' in. We describe the various features of visPIG and illustrate its utility with examples. visPIG is freely available through http://vispig.icr.ac.uk under a GNU General Public License (GPLv3).", "link"=>"http://www.mendeley.com/research/vispig-web-tool-producing-multiregion-multitrack-multiscale-plots-genetic-data", "reader_count"=>25, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>9, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>2, "Student > Master"=>3, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>9, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>2, "Student > Master"=>3, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>9, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>10, "Medicine and Dentistry"=>2, "Neuroscience"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Computer Science"=>{"Computer Science"=>2}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}}, "reader_count_by_country"=>{"United Kingdom"=>2, "Spain"=>1}, "group_count"=>2}

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• http://doi.org/10.1038/ncomms9690
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• http://doi.org/10.1186/s12859-017-1786-6
• http://doi.org/10.1038/ng.3823
• http://doi.org/10.1038/ncomms7178
• http://doi.org/10.1038/ncomms14175
• http://doi.org/10.1038/s41467-018-03178-z
• http://doi.org/10.1093/bfgp/elx012
• http://doi.org/10.1038/s41467-017-00320-1
• http://doi.org/10.1016/j.celrep.2016.07.053
• http://doi.org/10.1186/s12864-015-2140-x
• http://doi.org/10.1038/ncomms12050
• http://doi.org/10.1371/journal.pone.0122589
• http://doi.org/10.1038/ng.3896
• http://doi.org/10.1093/neuonc/noz088
• http://doi.org/10.1080/15384101.2017.1361068
• http://doi.org/10.1038/ncomms9559
• http://doi.org/10.1182/blood-2018-06-855296
• http://doi.org/10.1038/srep15065
• http://doi.org/10.1038/s41598-018-36560-4
• http://doi.org/10.1093/hmg/ddw087
• http://doi.org/10.3892/mmr.2017.7188
• http://doi.org/10.1002/1873-3468.12778
• http://doi.org/10.1038/ncomms14616
• http://doi.org/10.1093/neuonc/noy077
• http://doi.org/10.1038/s41467-019-09775-w
• http://doi.org/10.1021/acs.jafc.9b00970
• http://doi.org/10.1038/srep41071
• http://doi.org/10.1038/leu.2016.271
• http://doi.org/10.1016/j.surg.2017.01.032

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• {"id"=>"709426746408505344", "text"=>"#PLOSONE: visPIG - A Web Tool for Producing Multi-Region, Multi-Track, Multi-Scale Plots of Genetic Data https://t.co/n1wm3VF4vi", "created_at"=>"2016-03-14T17:11:31Z", "user"=>"amit_sud", "user_name"=>"Amit Sud", "user_profile_image"=>"http://pbs.twimg.com/profile_images/547464363531960320/DLeejy8U_normal.jpeg"}

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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

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Computer and information sciences/Data visualization", "average_usage"=>[330, 480]}, {"subject_area"=>"/Engineering and technology", "average_usage"=>[282]}, {"subject_area"=>"/Engineering and technology/Software engineering", "average_usage"=>[348, 519]}]}

F1000Prime