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Heatmapper specifications

Information


Unique identifier OMICS_12077
Name Heatmapper
Interface Web user interface
Restrictions to use None
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline David Wishart

Information


Unique identifier OMICS_12077
Name Heatmapper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline David Wishart

Publication for Heatmapper

Heatmapper citations

 (7)
call_split

Rb is required for retinal angiogenesis and lamination

2018
PMCID: 5840357
PMID: 29511172
DOI: 10.1038/s41419-018-0411-6
call_split See protocol

[…] EO website. The genes, of which expression fold changes are >2 or <0.5, and adjusted p < 0.05 were selected as the RbKO-related DEGs. Totally 677 DEGs were identified. The heatmap was generated using Heatmapper. The function enrichment of DEG was performed using Enrichr,, the pathways with adjusted p < 0.05 were chosen to report. […]

library_books

Comparative genomic and transcriptomic analyses of Family 1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress responsive regulation

2018
Sci Rep
PMCID: 5789830
PMID: 29382843
DOI: 10.1038/s41598-018-19535-3

[…] que, and stem, was obtained and analyzed according to the phylogenetic groups. A heatmap of the data was generated using the distance function (Euclidean) and hierarchical clustering (Average) on the Heatmapper website (http://heatmapper.ca/). To compare tissue-specific expression data of B. rapa, we analyzed the RNA-Seq and microarray data for expression of 118 UGTs across 10 developmental stages […]

library_books

Gene expression signature regulated by the KEAP1 NRF2 CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

2018
BMC Cancer
PMCID: 5756380
PMID: 29306329
DOI: 10.1186/s12885-017-3907-z

[…] ined from both datasets using ‘Venny 2.1’ (http://bioinfogp.cnb.csic.es/tools/venny/index.html) for further analysis. Hierarchical clustering of overlapping upregulated genes was performed using the ‘Heatmapper’ web tool []. Box plots of the overlapping upregulated genes that represent the log (counts per million) expression values were generated using R-package ‘ggplot2’ []. The overall workflow […]

library_books

Vacuolar protein sorting 13C is a novel lipid droplet protein that inhibits lipolysis in brown adipocytes

2017
PMCID: 5784322
PMID: 29175050
DOI: 10.1016/j.molmet.2017.10.014

[…] h ≥80% probability.The top 100 LD proteins in control samples were selected, spectral counts were normalized for total counts and converted to a log scale. Hierarchical clustering was performed using Heatmapper using Pearson complete linkage. […]

call_split

High Ambient Temperature Represses Anthocyanin Biosynthesis through Degradation of HY5

2017
Front Plant Sci
PMCID: 5655971
PMID: 29104579
DOI: 10.3389/fpls.2017.01787
call_split See protocol

[…] pressed genes (a total of 915 genes) were identified using the Plant GeneSet Enrichment Analysis Toolkit () and heat maps for the expression of the anthocyanin biosynthetic genes were generated using Heatmapper web-based tools (). […]

call_split

Genome wide identification and characterization of Glyceraldehyde 3 phosphate dehydrogenase genes family in wheat (Triticum aestivum)

2016
BMC Genomics
PMCID: 4793594
PMID: 26984398
DOI: 10.1186/s12864-016-2527-3
call_split See protocol

[…] n Genevestigator (https://genevestigator.com/gv/) [], the tissue expression profiles and the inducible expression profiles in response to stress of GAPDHs were generated by software OriginPro 9.1 and Heatmapper tool in the BAR (http://bar.utoronto.ca/ntools/cgi-bin/ntools_heatmapper.cgi). […]

Citations

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Heatmapper institution(s)
Department of Computing Science, University of Alberta, Edmonton, AB, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; National Institute for Nanotechnology, Edmonton, AB, Canada
Heatmapper funding source(s)
Supported by the Canadian Institutes of Health Research and Genome Alberta.

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