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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.


Database file system of HeatmapGenerator and software information. HeatmapGenerator can handle an unlimited number of heatmaps in its storage system. Software logo, licensure, copyright information, and user instructions are provided.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
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Fig4: Database file system of HeatmapGenerator and software information. HeatmapGenerator can handle an unlimited number of heatmaps in its storage system. Software logo, licensure, copyright information, and user instructions are provided.

Mentions: Some features of the GUI include a legend that is based on the data. The scaling parameters are developed based on the data that was supplied by the user. Also, the colors of the heatmap can be changed from simple buttons in order to specify a color scheme. After the user has run the HeatmapGenerator, the GUI is able to export the visualized heatmap in either.png or.jpg file formats that allow for publication-quality graphics. A.tiff image is always provided by the software by default. One additional feature is the ability to recall the previous heatmaps that were generated using a backend random access database. The user data is stored in a local database for easy recall and easy reusage to build the same heatmap in case the user wishes to reproduce the file. A user can store an unlimited number of heatmaps in the database file system, provided that these heatmaps reside within the same folder as the HeatmapGenerator program itself (refer to Figure 4).Figure 4


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)

Database file system of HeatmapGenerator and software information. HeatmapGenerator can handle an unlimited number of heatmaps in its storage system. Software logo, licensure, copyright information, and user instructions are provided.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Database file system of HeatmapGenerator and software information. HeatmapGenerator can handle an unlimited number of heatmaps in its storage system. Software logo, licensure, copyright information, and user instructions are provided.
Mentions: Some features of the GUI include a legend that is based on the data. The scaling parameters are developed based on the data that was supplied by the user. Also, the colors of the heatmap can be changed from simple buttons in order to specify a color scheme. After the user has run the HeatmapGenerator, the GUI is able to export the visualized heatmap in either.png or.jpg file formats that allow for publication-quality graphics. A.tiff image is always provided by the software by default. One additional feature is the ability to recall the previous heatmaps that were generated using a backend random access database. The user data is stored in a local database for easy recall and easy reusage to build the same heatmap in case the user wishes to reproduce the file. A user can store an unlimited number of heatmaps in the database file system, provided that these heatmaps reside within the same folder as the HeatmapGenerator program itself (refer to Figure 4).Figure 4

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.