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      ggbio: an R package for extending the grammar of graphics for genomic data

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      Author(s): 1 , 2 , 3 ,
      Publication date (Electronic):
      Journal: Genome Biology
      Publisher: BioMed Central

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          Abstract

          We introduce ggbio, a new methodology to visualize and explore genomics annotations and high-throughput data. The plots provide detailed views of genomic regions, summary views of sequence alignments and splicing patterns, and genome-wide overviews with karyogram, circular and grand linear layouts. The methods leverage the statistical functionality available in R, the grammar of graphics and the data handling capabilities of the Bioconductor project. The plots are specified within a modular framework that enables users to construct plots in a systematic way, and are generated directly from Bioconductor data structures. The ggbio R package is available at http://www.bioconductor.org/packages/2.11/bioc/html/ggbio.html.

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          The generic genome browser: a building block for a model organism system database.

          Lincoln D. Stein, Christopher John Mungall, ShengQiang Shu … (2002)
          The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.
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            Ensembl 2011

            Paul Flicek, M. Amode, Daniel Barrell … (2010)
            The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.
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              The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

              John Nicol, Gregg Helt, Steven Blanchard … (2009)
              Summary: Experimental techniques that survey an entire genome demand flexible, highly interactive visualization tools that can display new data alongside foundation datasets, such as reference gene annotations. The Integrated Genome Browser (IGB) aims to meet this need. IGB is an open source, desktop graphical display tool implemented in Java that supports real-time zooming and panning through a genome; layout of genomic features and datasets in moveable, adjustable tiers; incremental or genome-scale data loading from remote web servers or local files; and dynamic manipulation of quantitative data via genome graphs. Availability: The application and source code are available from http://igb.bioviz.org and http://genoviz.sourceforge.net. Contact: aloraine@uncc.edu
              Article 0 comments Cited 292 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Tengfei Yin
                Dianne Cook
                Michael Lawrence
                Journal
                Journal ID (nlm-ta): Genome Biol
                Journal ID (iso-abbrev): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2012
                Publication date (Electronic): 31 August 2012
                Volume: 13
                Issue: 8
                Page: R77
                Affiliations
                [1 ]Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
                [2 ]Department of Statistics, Iowa State University, Ames, IA 50011, USA
                [3 ]Department of Bioinformatics, Genentech, 1 Dna Way South San Francisco, CA 94080, USA
                Article
                Publisher ID: gb-2012-13-8-r77
                DOI: 10.1186/gb-2012-13-8-r77
                PMC ID: 4053745
                PubMed ID: 22937822
                SO-VID: bf22036f-66dd-4e44-8090-d60977a4590d
                Copyright © Copyright © 2012 Yin et al.; licensee BioMed Central Ltd.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 8 June 2012
                Date revision received : 17 July 2012
                Date accepted : 31 August 2012
                Categories
                Subject: Software

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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