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HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline.

Khomtchouk BB, Van Booven DJ, Wahlestedt C - Source Code Biol Med (2014)

Bottom Line: Advanced features such as color, text labels, scaling, legend construction, and even database storage can be easily customized with no prior programming knowledge.We provide an intuitive and user-friendly software package, HeatmapGenerator, to create high-quality, customizable heatmaps generated using the high-resolution color graphics capabilities of R.The software is available for Microsoft Windows and Apple Mac OS X.

View Article: PubMed Central - PubMed

Affiliation: Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th ST, Miami, 33136 FL USA.

ABSTRACT

Background: The graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research. Heatmaps are used extensively to plot quantitative differences in gene expression levels, such as those measured with RNAseq and microarray experiments, to provide qualitative large-scale views of the transcriptonomic landscape. Creating high-quality heatmaps is a computationally intensive task, often requiring considerable programming experience, particularly for customizing features to a specific dataset at hand.

Methods: Software to create publication-quality heatmaps is developed with the R programming language, C++ programming language, and OpenGL application programming interface (API) to create industry-grade high performance graphics.

Results: We create a graphical user interface (GUI) software package called HeatmapGenerator for Windows OS and Mac OS X as an intuitive, user-friendly alternative to researchers with minimal prior coding experience to allow them to create publication-quality heatmaps using R graphics without sacrificing their desired level of customization. The simplicity of HeatmapGenerator is that it only requires the user to upload a preformatted input file and download the publicly available R software language, among a few other operating system-specific requirements. Advanced features such as color, text labels, scaling, legend construction, and even database storage can be easily customized with no prior programming knowledge.

Conclusion: We provide an intuitive and user-friendly software package, HeatmapGenerator, to create high-quality, customizable heatmaps generated using the high-resolution color graphics capabilities of R. The software is available for Microsoft Windows and Apple Mac OS X. HeatmapGenerator is released under the GNU General Public License and publicly available at: http://sourceforge.net/projects/heatmapgenerator/. The Mac OS X direct download is available at: http://sourceforge.net/projects/heatmapgenerator/files/HeatmapGenerator_MAC_OSX.tar.gz/download. The Windows OS direct download is available at: http://sourceforge.net/projects/heatmapgenerator/files/HeatmapGenerator_WINDOWS.zip/download.

No MeSH data available.


Small input advanced heatmap generated by HeatmapGenerator. Advanced heatmap of a small input dataset is created by the graphical user interface of HeatmapGenerator.
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Related In: Results  -  Collection

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Fig2: Small input advanced heatmap generated by HeatmapGenerator. Advanced heatmap of a small input dataset is created by the graphical user interface of HeatmapGenerator.

Mentions: The HeatmapGenerator GUI design gives the user a full suite of options for creating, customizing, saving, storing, and choosing between simple and advanced heatmap construction. Running the HeatmapGenerator software package produces a variety of heatmaps (refer to Figure 2 and Figure 3) showing the relative expression levels of genes from either large or small datasets used as the input to the program. Simple input to the HeatmapGenerator can be as many as a few lines of a textfile up to thousands of lines of data in a textfile that are imported from a large array of analyses.Figure 2


HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline.

Khomtchouk BB, Van Booven DJ, Wahlestedt C - Source Code Biol Med (2014)

Small input advanced heatmap generated by HeatmapGenerator. Advanced heatmap of a small input dataset is created by the graphical user interface of HeatmapGenerator.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4279803&req=5

Fig2: Small input advanced heatmap generated by HeatmapGenerator. Advanced heatmap of a small input dataset is created by the graphical user interface of HeatmapGenerator.
Mentions: The HeatmapGenerator GUI design gives the user a full suite of options for creating, customizing, saving, storing, and choosing between simple and advanced heatmap construction. Running the HeatmapGenerator software package produces a variety of heatmaps (refer to Figure 2 and Figure 3) showing the relative expression levels of genes from either large or small datasets used as the input to the program. Simple input to the HeatmapGenerator can be as many as a few lines of a textfile up to thousands of lines of data in a textfile that are imported from a large array of analyses.Figure 2

Bottom Line: Advanced features such as color, text labels, scaling, legend construction, and even database storage can be easily customized with no prior programming knowledge.We provide an intuitive and user-friendly software package, HeatmapGenerator, to create high-quality, customizable heatmaps generated using the high-resolution color graphics capabilities of R.The software is available for Microsoft Windows and Apple Mac OS X.

View Article: PubMed Central - PubMed

Affiliation: Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th ST, Miami, 33136 FL USA.

ABSTRACT

Background: The graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research. Heatmaps are used extensively to plot quantitative differences in gene expression levels, such as those measured with RNAseq and microarray experiments, to provide qualitative large-scale views of the transcriptonomic landscape. Creating high-quality heatmaps is a computationally intensive task, often requiring considerable programming experience, particularly for customizing features to a specific dataset at hand.

Methods: Software to create publication-quality heatmaps is developed with the R programming language, C++ programming language, and OpenGL application programming interface (API) to create industry-grade high performance graphics.

Results: We create a graphical user interface (GUI) software package called HeatmapGenerator for Windows OS and Mac OS X as an intuitive, user-friendly alternative to researchers with minimal prior coding experience to allow them to create publication-quality heatmaps using R graphics without sacrificing their desired level of customization. The simplicity of HeatmapGenerator is that it only requires the user to upload a preformatted input file and download the publicly available R software language, among a few other operating system-specific requirements. Advanced features such as color, text labels, scaling, legend construction, and even database storage can be easily customized with no prior programming knowledge.

Conclusion: We provide an intuitive and user-friendly software package, HeatmapGenerator, to create high-quality, customizable heatmaps generated using the high-resolution color graphics capabilities of R. The software is available for Microsoft Windows and Apple Mac OS X. HeatmapGenerator is released under the GNU General Public License and publicly available at: http://sourceforge.net/projects/heatmapgenerator/. The Mac OS X direct download is available at: http://sourceforge.net/projects/heatmapgenerator/files/HeatmapGenerator_MAC_OSX.tar.gz/download. The Windows OS direct download is available at: http://sourceforge.net/projects/heatmapgenerator/files/HeatmapGenerator_WINDOWS.zip/download.

No MeSH data available.