Heatmapper protocols

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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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Maintainer


  • person_outline David Wishart <>

Publication for Heatmapper

Heatmapper in pipelines

 (2)
2018
PMCID: 5840357
PMID: 29511172
DOI: 10.1038/s41419-018-0411-6

[…] 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., total rna was isolated from dissected peripheral retina using […]

2017
PMCID: 5642521
PMID: 29050246
DOI: 10.18632/oncotarget.19349

[…] expression of genes was carried out in all triplicate samples and the genes that underwent up- or down-regulation were identified using a p-value <0.05 calculated using the t-test. we used a heatmapper tool [] to generate heat maps to depict up- and down-regulated genes., the david web tool [] was used to identify the functional annotation of downregulated genes (fold-change >1.5) […]

Heatmapper in publications

 (5)
PMCID: 5831854
PMID: 29490708
DOI: 10.1186/s40478-018-0524-2

[…] hierarchical clustering of individual clinical cases and the identified differentially expressed proteins was performed based on their relative protein abundances in each samples by using heatmapper online tool with an average linkage clustering and kendall’s tau distance measurement method []. protein expression heat map with dendrograms showing clustering results were generated […]

PMCID: 5767178
PMID: 29375519
DOI: 10.3389/fmicb.2017.02654

[…] pao1 cog mappings (http://www.pseudomonas.com). absolute expression comparisons were made using the regularized log transformation (rlog) in deseq2 (love et al., ). data were visualized using the heatmapper webtool (babicki et al., ), clustvis webtool (metsalu and vilo, ) and ggplot package in rstudio (wickham, )., the effects of individual qtee, qscr, or qsla gene deletions on the induction […]

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

[…] 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 […]

PMCID: 5716246
PMID: 29202709
DOI: 10.1186/s12870-017-1155-7

[…] dispersions were used to calculate differentially expressed genes with a false discovery rate of ≤ 0.05. clustering was carried out using cluster software package (version 3.0) and analysed using heatmapper []. go enrichment was performed using topgo (https://bioconductor.org/packages/release/bioc/html/topgo.html) enriched terms were assigned weighted p-values using fishers exact test., […]

PMCID: 5642521
PMID: 29050246
DOI: 10.18632/oncotarget.19349

[…] expression of genes was carried out in all triplicate samples and the genes that underwent up- or down-regulation were identified using a p-value <0.05 calculated using the t-test. we used a heatmapper tool [] to generate heat maps to depict up- and down-regulated genes., the david web tool [] was used to identify the functional annotation of downregulated genes (fold-change >1.5) […]

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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