ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation
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{"title"=>"ViVar: A comprehensive platform for the analysis and visualization of structural genomic variation", "type"=>"journal", "authors"=>[{"first_name"=>"Tom", "last_name"=>"Sante", "scopus_author_id"=>"36460159000"}, {"first_name"=>"Sarah", "last_name"=>"Vergult", "scopus_author_id"=>"35727343700"}, {"first_name"=>"Pieter Jan", "last_name"=>"Volders", "scopus_author_id"=>"55961825100"}, {"first_name"=>"Wigard P.", "last_name"=>"Kloosterman", "scopus_author_id"=>"8620072200"}, {"first_name"=>"Geert", "last_name"=>"Trooskens", "scopus_author_id"=>"8845374300"}, {"first_name"=>"Katleen", "last_name"=>"De Preter", "scopus_author_id"=>"6507009834"}, {"first_name"=>"Annelies", "last_name"=>"Dheedene", "scopus_author_id"=>"35101799400"}, {"first_name"=>"Frank", "last_name"=>"Speleman", "scopus_author_id"=>"35462081100"}, {"first_name"=>"Tim", "last_name"=>"De Meyer", "scopus_author_id"=>"23003898800"}, {"first_name"=>"Björn", "last_name"=>"Menten", "scopus_author_id"=>"6505972689"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84917695118", "pmid"=>"25503062", "sgr"=>"84917695118", "doi"=>"10.1371/journal.pone.0113800", "isbn"=>"1932-6203", "issn"=>"19326203", "pui"=>"600756284"}, "id"=>"0848c638-8508-3d1c-a36e-342dd03ec732", "abstract"=>"Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist to handle different parts and aspects of such sequencing based structural variation analyses pipelines. A comprehensive analysis platform to handle all steps, from processing the sequencing data, to the discovery and visualization of structural variants, is missing. The ViVar platform is built to handle the discovery of structural variants, from Depth Of Coverage analysis, aberrant read pair clustering to split read analysis. ViVar provides you with powerful visualization options, enables easy reporting of results and better usability and data management. The platform facilitates the processing, analysis and visualization, of structural variation based on massive parallel sequencing data, enabling the rapid identification of disease loci or genes. ViVar allows you to scale your analysis with your work load over multiple (cloud) servers, has user access control to keep your data safe and is easy expandable as analysis techniques advance. URL: https://www.cmgg.be/vivar/", "link"=>"http://www.mendeley.com/research/vivar-comprehensive-platform-analysis-visualization-structural-genomic-variation", "reader_count"=>38, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>1, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>1, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>13, "Mathematics"=>1, "Medicine and Dentistry"=>5, "Agricultural and Biological Sciences"=>13, "Business, Management and Accounting"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Computer Science"=>{"Computer Science"=>2}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "Belgium"=>1, "China"=>1, "Japan"=>1, "Denmark"=>1, "France"=>2}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1841630"], "description"=>"<p>View an overview of all experiments for a case/patient with a complex trisomy 21.</p>", "links"=>[], "tags"=>["Structural Genomic Variation Structural genomic variations", "ViVar", "visualization", "platform", "variation analyses pipelines", "url", "sequencing data", "Several analysis tools", "user access control", "analysis techniques advance"], "article_id"=>1269488, "categories"=>["Biological Sciences"], "users"=>["Tom Sante", "Sarah Vergult", "Pieter-Jan Volders", "Wigard P. Kloosterman", "Geert Trooskens", "Katleen De Preter", "Annelies Dheedene", "Frank Speleman", "Tim De Meyer", "Björn Menten"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113800.g005", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Report_/1269488", "title"=>"Report.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-12 02:49:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1841624"], "description"=>"<p>Illustration of the criteria to determine similarity when grouping pairs in clusters: pair <i>i</i> is considered to be part of a cluster if the start position of the first (α<sub>i</sub>) and second read (β<sub>i</sub>) of the pair is within a region centered on the mean start position of all reads in start (µ<sup>α</sup><sub>k</sub>) and end (µ<sup>β</sup><sub>k</sub>) of the cluster <i>k</i> and extended left and right with twice the standard deviation of the mean insert size calculated for all pairs in the sample (σ<sub>IS</sub>). Pair <i>i</i> is member of cluster <i>k</i><b>if</b><b><b><b>and</b></b></b>.</p>", "links"=>[], "tags"=>["Structural Genomic Variation Structural genomic variations", "ViVar", "visualization", "platform", "variation analyses pipelines", "url", "sequencing data", "Several analysis tools", "user access control", "analysis techniques advance"], "article_id"=>1269482, "categories"=>["Biological Sciences"], "users"=>["Tom Sante", "Sarah Vergult", "Pieter-Jan Volders", "Wigard P. Kloosterman", "Geert Trooskens", "Katleen De Preter", "Annelies Dheedene", "Frank Speleman", "Tim De Meyer", "Björn Menten"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113800.g001", "stats"=>{"downloads"=>3, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_/1269482", "title"=>"Clustering.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-12 02:49:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1841625"], "description"=>"<p>(top) sequencing data based coverage and clustering information (bottom) genomic microarray profile. Aberrant clusters are depicted as red arches. Horizontal segments delineate coverage windows in case of sequencing data or microarray probes in case of genomic-microarray/arrayCGH data, segment can be colored in blue when indicating a gain or red for a loss. Below the ratio, cluster plot of the samples, 2 chromosome arms are draw with segmental duplications shown between them. The lower part contains the annotation tracks.</p>", "links"=>[], "tags"=>["Structural Genomic Variation Structural genomic variations", "ViVar", "visualization", "platform", "variation analyses pipelines", "url", "sequencing data", "Several analysis tools", "user access control", "analysis techniques advance"], "article_id"=>1269483, "categories"=>["Biological Sciences"], "users"=>["Tom Sante", "Sarah Vergult", "Pieter-Jan Volders", "Wigard P. Kloosterman", "Geert Trooskens", "Katleen De Preter", "Annelies Dheedene", "Frank Speleman", "Tim De Meyer", "Björn Menten"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113800.g002", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chromosome_view_a_patient_with_a_complex_trisomy_21_/1269483", "title"=>"Chromosome view, a patient with a complex trisomy 21.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-12 02:49:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1841626"], "description"=>"<p>Karyoview, showing a karyogram of a patient with a complex trisomy 21.</p>", "links"=>[], "tags"=>["Structural Genomic Variation Structural genomic variations", "ViVar", "visualization", "platform", "variation analyses pipelines", "url", "sequencing data", "Several analysis tools", "user access control", "analysis techniques advance"], "article_id"=>1269484, "categories"=>["Biological Sciences"], "users"=>["Tom Sante", "Sarah Vergult", "Pieter-Jan Volders", "Wigard P. Kloosterman", "Geert Trooskens", "Katleen De Preter", "Annelies Dheedene", "Frank Speleman", "Tim De Meyer", "Björn Menten"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113800.g003", "stats"=>{"downloads"=>6, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Karyoview_showing_a_karyogram_of_a_patient_with_a_complex_trisomy_21_/1269484", "title"=>"Karyoview, showing a karyogram of a patient with a complex trisomy 21.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-12 02:49:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1841628"], "description"=>"<p>Heatmap, plotting copy number variants for two sequencing and two genomic microarray based experiments.</p>", "links"=>[], "tags"=>["Structural Genomic Variation Structural genomic variations", "ViVar", "visualization", "platform", "variation analyses pipelines", "url", "sequencing data", "Several analysis tools", "user access control", "analysis techniques advance"], "article_id"=>1269486, "categories"=>["Biological Sciences"], "users"=>["Tom Sante", "Sarah Vergult", "Pieter-Jan Volders", "Wigard P. Kloosterman", "Geert Trooskens", "Katleen De Preter", "Annelies Dheedene", "Frank Speleman", "Tim De Meyer", "Björn Menten"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0113800.g004", "stats"=>{"downloads"=>4, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heatmap_plotting_copy_number_variants_for_two_sequencing_and_two_genomic_microarray_based_experiments_/1269486", "title"=>"Heatmap, plotting copy number variants for two sequencing and two genomic microarray based experiments.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-12 02:49:57"}

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