GenomeGraphs: integrated genomic data visualization with R.

Steffen Durinck, James Bullard, Paul Spellman, Sandrine Dudoit

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2
Number of pages1
JournalBMC Bioinformatics
Volume10
DOIs
StatePublished - 2009
Externally publishedYes

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Data visualization
Data Visualization
Software packages
Genomics
Visualization
Software
Computer programming
Annotation
Genes
Throughput
Programming Environments
Experimental Data
Software Package
Experiments
Datasets
High Throughput
Data analysis
Query
Gene
Grid

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

GenomeGraphs : integrated genomic data visualization with R. / Durinck, Steffen; Bullard, James; Spellman, Paul; Dudoit, Sandrine.

In: BMC Bioinformatics, Vol. 10, 2009, p. 2.

Research output: Contribution to journalArticle

Durinck, Steffen ; Bullard, James ; Spellman, Paul ; Dudoit, Sandrine. / GenomeGraphs : integrated genomic data visualization with R. In: BMC Bioinformatics. 2009 ; Vol. 10. pp. 2.
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