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{"title"=>"HemI: A toolkit for illustrating heatmaps", "type"=>"journal", "authors"=>[{"first_name"=>"Wankun", "last_name"=>"Deng", "scopus_author_id"=>"55813358100"}, {"first_name"=>"Yongbo", "last_name"=>"Wang", "scopus_author_id"=>"54394438100"}, {"first_name"=>"Zexian", "last_name"=>"Liu", "scopus_author_id"=>"55632837400"}, {"first_name"=>"Han", "last_name"=>"Cheng", "scopus_author_id"=>"55378479600"}, {"first_name"=>"Yu", "last_name"=>"Xue", "scopus_author_id"=>"7402270422"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84910655736", "pui"=>"600436066", "doi"=>"10.1371/journal.pone.0111988", "isbn"=>"1932-6203", "sgr"=>"84910655736", "pmid"=>"25372567"}, "id"=>"a9206794-be58-31fc-9baa-c629d6d13f01", "abstract"=>"Recent high-throughput techniques have generated a flood of biological data in all aspects. The transformation and visualization of multi-dimensional and numerical gene or protein expression data in a single heatmap can provide a concise but comprehensive presentation of molecular dynamics under different conditions. In this work, we developed an easy-to-use tool named HemI (Heat map Illustrator), which can visualize either gene or protein expression data in heatmaps. Additionally, the heatmaps can be recolored, rescaled or rotated in a customized manner. In addition, HemI provides multiple clustering strategies for analyzing the data. Publication-quality figures can be exported directly. We propose that HemI can be a useful toolkit for conveniently visualizing and manipulating heatmaps. The stand-alone packages of HemI were implemented in Java and can be accessed at http://hemi.biocuckoo.org/down.php.", "link"=>"http://www.mendeley.com/research/hemi-toolkit-illustrating-heatmaps", "reader_count"=>59, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>3, "Researcher"=>13, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>2, "Student > Master"=>13, "Other"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>3, "Researcher"=>13, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>2, "Student > Master"=>13, "Other"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>12, "Agricultural and Biological Sciences"=>31, "Medicine and Dentistry"=>2, "Neuroscience"=>1, "Sports and Recreations"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Physics and Astronomy"=>1, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Argentina"=>1, "China"=>4, "South Africa"=>2, "Spain"=>1}, "group_count"=>1}

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• {"month"=>"5", "year"=>"2016", "pdf_views"=>"123", "xml_views"=>"0", "html_views"=>"137"}
• {"month"=>"6", "year"=>"2016", "pdf_views"=>"102", "xml_views"=>"0", "html_views"=>"115"}
• {"month"=>"7", "year"=>"2016", "pdf_views"=>"91", "xml_views"=>"0", "html_views"=>"115"}
• {"month"=>"8", "year"=>"2016", "pdf_views"=>"105", "xml_views"=>"0", "html_views"=>"124"}
• {"month"=>"9", "year"=>"2016", "pdf_views"=>"117", "xml_views"=>"0", "html_views"=>"149"}
• {"month"=>"10", "year"=>"2016", "pdf_views"=>"128", "xml_views"=>"0", "html_views"=>"145"}
• {"month"=>"11", "year"=>"2016", "pdf_views"=>"59", "xml_views"=>"0", "html_views"=>"140"}
• {"month"=>"12", "year"=>"2016", "pdf_views"=>"163", "xml_views"=>"0", "html_views"=>"183"}
• {"month"=>"1", "year"=>"2017", "pdf_views"=>"93", "xml_views"=>"1", "html_views"=>"153"}
• {"month"=>"2", "year"=>"2017", "pdf_views"=>"85", "xml_views"=>"4", "html_views"=>"139"}
• {"month"=>"3", "year"=>"2017", "pdf_views"=>"132", "xml_views"=>"1", "html_views"=>"200"}
• {"month"=>"4", "year"=>"2017", "pdf_views"=>"105", "xml_views"=>"1", "html_views"=>"151"}
• {"month"=>"5", "year"=>"2017", "pdf_views"=>"107", "xml_views"=>"0", "html_views"=>"147"}
• {"month"=>"6", "year"=>"2017", "pdf_views"=>"105", "xml_views"=>"1", "html_views"=>"142"}
• {"month"=>"7", "year"=>"2017", "pdf_views"=>"118", "xml_views"=>"2", "html_views"=>"118"}
• {"month"=>"8", "year"=>"2017", "pdf_views"=>"96", "xml_views"=>"2", "html_views"=>"131"}
• {"month"=>"9", "year"=>"2017", "pdf_views"=>"94", "xml_views"=>"0", "html_views"=>"126"}
• {"month"=>"10", "year"=>"2017", "pdf_views"=>"97", "xml_views"=>"2", "html_views"=>"151"}
• {"month"=>"11", "year"=>"2017", "pdf_views"=>"91", "xml_views"=>"1", "html_views"=>"166"}
• {"month"=>"12", "year"=>"2017", "pdf_views"=>"124", "xml_views"=>"2", "html_views"=>"191"}
• {"month"=>"1", "year"=>"2018", "pdf_views"=>"143", "xml_views"=>"0", "html_views"=>"121"}
• {"month"=>"2", "year"=>"2018", "pdf_views"=>"64", "xml_views"=>"3", "html_views"=>"63"}
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• {"month"=>"5", "year"=>"2018", "pdf_views"=>"120", "xml_views"=>"1", "html_views"=>"112"}
• {"month"=>"6", "year"=>"2018", "pdf_views"=>"100", "xml_views"=>"3", "html_views"=>"129"}
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• {"month"=>"8", "year"=>"2018", "pdf_views"=>"111", "xml_views"=>"3", "html_views"=>"98"}
• {"month"=>"9", "year"=>"2018", "pdf_views"=>"94", "xml_views"=>"1", "html_views"=>"89"}
• {"month"=>"10", "year"=>"2018", "pdf_views"=>"84", "xml_views"=>"1", "html_views"=>"59"}

Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1779467"], "description"=>"a<p>Tools, the name of used tools;</p>b<p>Num., the number of papers that used the tool;</p>c<p>Web link, the website of the tool;</p>d<p>N/A, not mentioned in the corresponding papers.</p><p>The summarization of the methods for illustrating heatmaps among the 202 papers published in 2012 on five leading journals.</p>", "links"=>[], "tags"=>["hemi", "protein expression data", "heatmap", "Illustrating Heatmaps", "gene"], "article_id"=>1229168, "categories"=>["Biological Sciences"], "users"=>["Wankun Deng", "Yongbo Wang", "Zexian Liu", "Han Cheng", "Yu Xue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111988.t002", "stats"=>{"downloads"=>7, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_summarization_of_the_methods_for_illustrating_heatmaps_among_the_202_papers_published_in_2012_on_five_leading_journals_/1229168", "title"=>"The summarization of the methods for illustrating heatmaps among the 202 papers published in 2012 on five leading journals.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-05 03:08:55"}
• {"files"=>["https://ndownloader.figshare.com/files/1779468"], "description"=>"<p>To calculate the pairwise distances for the hierarchical clustering, three commonly used linkage criteria were taken from the Wikipedia (<a href=\"http://en.wikipedia.org/wiki/Hierarchical_clustering\" target=\"_blank\">http://en.wikipedia.org/wiki/Hierarchical_clustering</a>).</p><p>Three mostly used linkage criteria for the hierarchical clustering.</p>", "links"=>[], "tags"=>["hemi", "protein expression data", "heatmap", "Illustrating Heatmaps", "gene"], "article_id"=>1229169, "categories"=>["Biological Sciences"], "users"=>["Wankun Deng", "Yongbo Wang", "Zexian Liu", "Han Cheng", "Yu Xue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111988.t003", "stats"=>{"downloads"=>8, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Three_mostly_used_linkage_criteria_for_the_hierarchical_clustering_/1229169", "title"=>"Three mostly used linkage criteria for the hierarchical clustering.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-05 03:08:55"}
• {"files"=>["https://ndownloader.figshare.com/files/1779469"], "description"=>"<p>To calculate the distances for the hierarchical and k-means clustering approaches, up to 7 mostly used distances were adopted.</p><p>Seven distances for the clustering.</p>", "links"=>[], "tags"=>["hemi", "protein expression data", "heatmap", "Illustrating Heatmaps", "gene"], "article_id"=>1229170, "categories"=>["Biological Sciences"], "users"=>["Wankun Deng", "Yongbo Wang", "Zexian Liu", "Han Cheng", "Yu Xue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111988.t004", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Seven_distances_for_the_clustering_/1229170", "title"=>"Seven distances for the clustering.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-05 03:08:55"}
• {"files"=>["https://ndownloader.figshare.com/files/1779462"], "description"=>"<p>(A) The numerical data in one of three file formats can be directly loaded, whereas the data area can be selected by dragging or holding-SHIFT-then-click manipulations. Titles for <i>X</i>-axis or <i>Y</i>-axis can also be specified; (B) Multiple options for manipulating the heatmp; (C) The numeric data can be clustered for either or both of <i>X</i>-axis and <i>Y</i>-axis; (D) Publication-quality figures can be exported, and two figure formats were supported.</p>", "links"=>[], "tags"=>["hemi", "protein expression data", "heatmap", "Illustrating Heatmaps", "gene"], "article_id"=>1229163, "categories"=>["Biological Sciences"], "users"=>["Wankun Deng", "Yongbo Wang", "Zexian Liu", "Han Cheng", "Yu Xue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111988.g001", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Usage_of_HemI_1_0_/1229163", "title"=>"Usage of HemI 1.0.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-05 03:08:55"}
• {"files"=>["https://ndownloader.figshare.com/files/1779464"], "description"=>"<p>(A) Thermal shifts, which indicate binding affinities of 185 compounds to 13 PARPs, were measured by DSF. A higher value represents a stronger binding affinity. (B) Totally, 428 androgen-repressed genes were identified from LNCaP cells, after the treatment of 1 nM synthetic androgen R1881 for 3, 6, 12, 24 and 48 hours. Values shown were normalized to 0 hour and log² transformed.</p>", "links"=>[], "tags"=>["hemi", "protein expression data", "heatmap", "Illustrating Heatmaps", "gene"], "article_id"=>1229165, "categories"=>["Biological Sciences"], "users"=>["Wankun Deng", "Yongbo Wang", "Zexian Liu", "Han Cheng", "Yu Xue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111988.g002", "stats"=>{"downloads"=>2, "page_views"=>74, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustrating_heatmaps_by_HemI_1_0_/1229165", "title"=>"Illustrating heatmaps by HemI 1.0.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-05 03:08:55"}
• {"files"=>["https://ndownloader.figshare.com/files/1779465"], "description"=>"<p>To estimate <i>how</i> many papers contain heatmaps, we went through all original research papers (excluding reviews and other articles) published in 2012 of five leading journals as below.</p>a<p>Num. of Heatmaps, the number of papers containing with at least one heatmap figure;</p>b<p>Per., the percentiles.</p><p>Using frequency of heatmap.</p>", "links"=>[], "tags"=>["hemi", "protein expression data", "heatmap", "Illustrating Heatmaps", "gene"], "article_id"=>1229167, "categories"=>["Biological Sciences"], "users"=>["Wankun Deng", "Yongbo Wang", "Zexian Liu", "Han Cheng", "Yu Xue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111988.t001", "stats"=>{"downloads"=>3, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Using_frequency_of_heatmap_/1229167", "title"=>"Using frequency of heatmap.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-05 03:08:55"}

PMC Usage Stats | Further Information

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• {"unique-ip"=>"25", "full-text"=>"27", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
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• {"unique-ip"=>"27", "full-text"=>"20", "pdf"=>"13", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"12"}
• {"unique-ip"=>"29", "full-text"=>"20", "pdf"=>"11", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"1"}
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• {"unique-ip"=>"32", "full-text"=>"30", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
• {"unique-ip"=>"34", "full-text"=>"31", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"8"}
• {"unique-ip"=>"28", "full-text"=>"28", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
• {"unique-ip"=>"41", "full-text"=>"77", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
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• {"unique-ip"=>"45", "full-text"=>"43", "pdf"=>"11", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"14", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
• {"unique-ip"=>"30", "full-text"=>"32", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
• {"unique-ip"=>"59", "full-text"=>"62", "pdf"=>"13", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"14", "supp-data"=>"0", "cited-by"=>"2", "year"=>"2017", "month"=>"2"}
• {"unique-ip"=>"54", "full-text"=>"58", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"29", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
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• {"unique-ip"=>"23", "full-text"=>"23", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"13", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"7"}
• {"unique-ip"=>"44", "full-text"=>"39", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"14", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2017", "month"=>"8"}
• {"unique-ip"=>"50", "full-text"=>"46", "pdf"=>"16", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"27", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
• {"unique-ip"=>"59", "full-text"=>"54", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"29", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
• {"unique-ip"=>"47", "full-text"=>"46", "pdf"=>"13", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2017", "month"=>"11"}
• {"unique-ip"=>"53", "full-text"=>"45", "pdf"=>"21", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"10", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
• {"unique-ip"=>"41", "full-text"=>"29", "pdf"=>"13", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"29", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
• {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"2"}
• {"unique-ip"=>"59", "full-text"=>"42", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"16", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}

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"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[282]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[341, 529]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[306, 482]}, {"subject_area"=>"/Computer and information sciences", "average_usage"=>[327, 511]}, {"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