We are analyzing https://link.springer.com/article/10.1186/1471-2105-10-2.

Title:
GenomeGraphs: integrated genomic data visualization with R | BMC Bioinformatics
Description:
Background Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. Results We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. Conclusion GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.
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Keywords {🔍}

data, genomic, annotation, exon, genome, package, ensembl, genomegraphs, array, biomart, visualization, article, plot, class, software, gene, datasets, region, google, scholar, information, number, statistical, transcript, pubmed, integrated, plotted, figure, track, analysis, end, location, access, gdobject, copy, authors, durinck, biological, experimental, database, sequencing, plotting, dataset, object, affymetrix, minbase, maxbase, research, open, visualize,

Topics {✒️}

semi-transparent box highlights ultra high-throughput sequencing article download pdf related subjects distinct high-throughput experiments tiling array experiments google scholar conduct statistical analysis tiling array data copy number data represents strand-specific genes privacy choices/manage cookies additional classes exist exon array tracks alternative transcript isoforms authors’ original file custom genome annotation microarray data analysis copy number segments short read sequencing facilitate joint analysis genome annotation retrieval exon array data grid graphics package high-throughput assays custom annotation tracks relevant genome annotation bmc bioinformatics 2005 bmc bioinformatics 10 genomic coordinate axis article number 2 ensembl genome browser quantitative genomic data genomic annotation encoded high-resolution map genomic coordinate system red marker highlights genomic data type full access association data high-resolution atlas genomic annotation information custom annotation track dynamic biological networks biological databases draw biological conclusions software packages xml alternatively spliced exon integrated genomegraphs graphic article durinck

Schema {🗺️}

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         headline:GenomeGraphs: integrated genomic data visualization with R
         description:Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.
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      headline:GenomeGraphs: integrated genomic data visualization with R
      description:Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses. We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system. GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.
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         Computer Appl. in Life Sciences
         Algorithms
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