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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.


An example of a textfile for input as a matrix. A simple exemplary input file to be processed by HeatmapGenerator.
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Fig1: An example of a textfile for input as a matrix. A simple exemplary input file to be processed by HeatmapGenerator.

Mentions: For best use, we refer the reader to the operating system-specific “HeatmapGenerator manual.pdf” file that comes bundled with the HeatmapGenerator download. As stated in this file, to properly use the HeatmapGenerator software package, the user must first download R for (Mac)OSX/Windows at http://cran.rstudio.com/ and preformat the input file to be a tab-delimited textfile (.txt) (an example is provided as EXAMPLE.txt in the HeatmapGenerator download). Specifically, the input file should be a.txt file where each entry is separated by tabs, the first column should contain the item names (e.g., list of gene names), and the other columns should contain numbers corresponding to the respective items. An example of a.txt file table to be imported into HeatmapGenerator is shown in (refer to Figure 1). Note that each column is labeled with its respective header (e.g., Gene Name, Control 1, Exp 1, etc.).Figure 1


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)

An example of a textfile for input as a matrix. A simple exemplary input file to be processed by HeatmapGenerator.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: An example of a textfile for input as a matrix. A simple exemplary input file to be processed by HeatmapGenerator.
Mentions: For best use, we refer the reader to the operating system-specific “HeatmapGenerator manual.pdf” file that comes bundled with the HeatmapGenerator download. As stated in this file, to properly use the HeatmapGenerator software package, the user must first download R for (Mac)OSX/Windows at http://cran.rstudio.com/ and preformat the input file to be a tab-delimited textfile (.txt) (an example is provided as EXAMPLE.txt in the HeatmapGenerator download). Specifically, the input file should be a.txt file where each entry is separated by tabs, the first column should contain the item names (e.g., list of gene names), and the other columns should contain numbers corresponding to the respective items. An example of a.txt file table to be imported into HeatmapGenerator is shown in (refer to Figure 1). Note that each column is labeled with its respective header (e.g., Gene Name, Control 1, Exp 1, etc.).Figure 1

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.