Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Unlike existing non-commercial heat map packages, which either lack graphical interfaces or are specialized for only one or two kinds of heat maps, Heatmapper is a versatile tool that allows users to easily create a wide variety of heat maps for many different data types and applications. Heatmapper supports various types of heat maps, including expression-based heat maps from transcriptomic, proteomic and metabolomic experiments, pairwise distance maps, correlation maps, image overlay heat maps, latitude and longitude heat maps, and geopolitical (choropleth) heat maps. It offers simple and intuitive customization options for adjusting each heat map's appearance and plotting parameters. Users can interactively explore their numeric data values by hovering their cursor over each heat map cell or using a searchable/sortable data table view. Heat map data can be uploaded in text, Excel or tab delimited formats and the resulting heat map images can be downloaded in common formats including PNG, JPG and PDF. Heatmapper is designed to appeal to a wide range of users, including molecular biologists, structural biologists, microbiologists, epidemiologists, environmental scientists, agriculture/forestry scientists, fish and wildlife biologists, climatologists, geologists, educators and students. Heatmapper is available at http://www.heatmapper.ca. Heatmapper supports five different classes or types of heat maps: (i) Expression Heat Maps, (ii) Pairwise Comparison Heat Maps, (iii) Image Overlay Heat Maps, (iv) Geomap Heat Maps and (v) Geodensity Heat Maps. Each heat map type has its own specific features and uses. Expression Heat Maps are used for gene, protein and/or metabolite expression analysis. Pairwise Comparison Heat Maps are used for mapping geometric distances, linkage disequilibrium distances, taxonomic distances, or performing correlation mapping. Image Overlay Heat Maps allow users to overlay quantitative data on custom images. Geomap Heat Maps are used for mapping quantitative data onto geopolitical images. Geodensity Heat Maps are used for mapping data on geospatial coordinates. Heatmapper offers a number of simple and intuitive customization options for facile adjustments to each heat map's appearance and interactive querying of each heat map's numerical data content. Heatmapper is designed to appeal to a wide range of users, including molecular biologists, structural biologists, microbiologists, epidemiologists, environmental scientists, agriculture/forestry scientists, fish and wildlife biologists, climatologists, geologists and even social/political scientists. Heatmapper is implemented using Shiny (version 0.12.2), a framework for R (version 3.2.0). Tooltips are displayed using the shinyBS package. The custom colour selection widgets were generated using the jscolourR package. The spinner displayed on the screen when a page is loading is generated by the spin package. AllHeatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Unlike existing non-commercial heat map packages, which either lack graphical interfaces or are specialized for only one or two kinds of heat maps, Heatmapper is a versatile tool that allows users to easily create a wide variety of heat maps for many different data types and applications. Heatmapper supports various types of heat maps, including expression-based heat maps from transcriptomic, proteomic and metabolomic experiments, pairwise distance maps, correlation maps, image overlay heat maps, latitude and longitude heat maps, and geopolitical (choropleth) heat maps. It offers simple and intuitive customization options for adjusting each heat map's appearance and plotting parameters. Users can interactively explore their numeric data values by hovering their cursor over each heat map cell or using a searchable/sortable data table view. Heat map data can be uploaded in text, Excel or tab delimited formats and the resulting heat map images can be downloaded in common formats including PNG, JPG and PDF. Heatmapper is designed to appeal to a wide range of users, including molecular biologists, structural biologists, microbiologists, epidemiologists, environmental scientists, agriculture/forestry scientists, fish and wildlife biologists, climatologists, geologists, educators and students. Heatmapper is available at http://www.heatmapper.ca. Heatmapper supports five different classes or types of heat maps: (i) Expression Heat Maps, (ii) Pairwise Comparison Heat Maps, (iii) Image Overlay Heat Maps, (iv) Geomap Heat Maps and (v) Geodensity Heat Maps. Each heat map type has its own specific features and uses. Expression Heat Maps are used for gene, protein and/or metabolite expression analysis. Pairwise Comparison Heat Maps are used for mapping geometric distances, linkage disequilibrium distances, taxonomic distances, or performing correlation mapping. Image Overlay Heat Maps allow users to overlay quantitative data on custom images. Geomap Heat Maps are used for mapping quantitative data onto geopolitical images. Geodensity Heat Maps are used for mapping data on geospatial coordinates. Heatmapper offers a number of simple and intuitive customization options for facile adjustments to each heat map's appearance and interactive querying of each heat map's numerical data content. Heatmapper is designed to appeal to a wide range of users, including molecular biologists, structural biologists, microbiologists, epidemiologists, environmental scientists, agriculture/forestry scientists, fish and wildlife biologists, climatologists, geologists and even social/political scientists. Heatmapper is implemented using Shiny (version 0.12.2), a framework for R (version 3.2.0). Tooltips are displayed using the shinyBS package. The custom colour selection widgets were generated using the jscolourR package. The spinner displayed on the screen when a page is loading is generated by the spin package. All