GenomeGraphs: integrated genomic data visualization with R. Export

@article{citeulike:3851767, 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.}, author = {Durinck, Steffen and Bullard, James and Spellman, Paul T. and Dudoit, Sandrine}, citeulike-article-id = {3851767}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-10-2}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19123956}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19123956}, doi = {10.1186/1471-2105-10-2}, issn = {1471-2105}, journal = {BMC bioinformatics}, keywords = {genomics, graph, ma, r}, number = {1}, posted-at = {2009-01-27 07:55:25}, priority = {2}, title = {GenomeGraphs: integrated genomic data visualization with R.}, url = {http://dx.doi.org/10.1186/1471-2105-10-2}, volume = {10}, year = {2009} }

TY - JOUR ID - citeulike:3851767 L3 - citeulike-article-id:3851767 N2 - 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. IS - 1 JF - BMC bioinformatics SN - 1471-2105 TI - GenomeGraphs: integrated genomic data visualization with R. VL - 10 KW - genomics KW - graph KW - ma KW - r AU - Durinck, Steffen AU - Bullard, James AU - Spellman, Paul AU - Dudoit, Sandrine PY - 2009/// UR - http://dx.doi.org/10.1186/1471-2105-10-2 ER -