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Result: Heatmapper2: web-enabled heat mapping made easy.

Title:
Heatmapper2: web-enabled heat mapping made easy.
Authors:
Kernick K; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada., Woudstra R; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada., Berjanskii M; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada., MacKay S; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada., Wishart DS; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2E9, Canada.; Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E9, Canada.; Department of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Source:
Nucleic acids research [Nucleic Acids Res] 2025 Jul 07; Vol. 53 (W1), pp. W316-W323.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
Imprint Name(s):
Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
MeSH Terms:
Software*, Internet ; Humans ; Computer Graphics
References:
Nat Struct Biol. 2003 Dec;10(12):980. (PMID: 14634627)
Bioinformatics. 2009 Jun 1;25(11):1422-3. (PMID: 19304878)
Nat Methods. 2022 Feb;19(2):171-178. (PMID: 35102346)
Genome Biol. 2018 Feb 6;19(1):15. (PMID: 29409532)
Nat Methods. 2020 Mar;17(3):261-272. (PMID: 32015543)
Nucleic Acids Res. 2016 Jul 8;44(W1):W147-53. (PMID: 27190236)
Stem Cells. 1994 Jan;12(1):13-22. (PMID: 8142917)
Bioinformatics. 2015 Apr 15;31(8):1322-4. (PMID: 25505090)
Front Oncol. 2022 Jun 29;12:890410. (PMID: 35847846)
Bioinformatics. 2018 Jul 15;34(14):2513-2514. (PMID: 29394323)
Source Code Biol Med. 2014 Dec 24;9(1):30. (PMID: 25550709)
Nature. 2020 Sep;585(7825):357-362. (PMID: 32939066)
Grant Information:
Canada Foundation for Innovation; Genome Alberta
Entry Date(s):
Date Created: 20250505 Date Completed: 20250707 Latest Revision: 20250709
Update Code:
20250709
PubMed Central ID:
PMC12230736
DOI:
10.1093/nar/gkaf385
PMID:
40322914
Database:
MEDLINE

Further information

First released in 2016, Heatmapper provided the first comprehensive, web-based platform for easily visualizing and manipulating heat maps for a wide range of applications in biology, epidemiology, ecology, and many other areas of science and social science. However, as Heatmapper's popularity grew, limitations in its performance and functionality became more apparent, necessitating the development of a new version: Heatmapper2 (https://heatmapper2.ca/). Heatmapper2 represents a substantial upgrade to the original Heatmapper web server, with much of the code being completely rewritten to improve performance, enhance capabilities and integrate new web technologies. Among the key changes are the conversion of the back-end code from R to Python (for better processing speed), the migration away from R Shiny to Shiny Python, and the use of WebAssembly. WebAssembly enables high performance, graphically intense applications to be run client-side in a web browser. Moving computationally intense calculations away from a central server and on to client computers eliminates server congestion and significantly improves performance. In addition to its significantly improved performance, Heatmapper2 now supports a wider range of heat mapping options including: time-series or animated heat maps (for geospatial applications), 3D heat maps (for mapping data on organisms or body parts); protein structure heat maps (for mapping molecular dynamic processes), molecular spatial heat maps (for spatial omics applications), and spectrometric heat maps (for mass spectrometry applications). Heatmapper2's redesigned interface also supports much more extensive customization, more easily editable tables, and more efficient handling of large datasets. These enhancements should make Heatmapper2 much more appealing for a wider range of researchers and research applications.
(© The Author(s) 2025. Published by Oxford University Press on behalf of Nucleic Acids Research.)