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Complex heatmaps specifications


Unique identifier OMICS_12421
Name Complex heatmaps
Alternative name ComplexHeatmap
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.11.4
Stability Stable
Maintained Yes




No version available



  • person_outline Matthias Schlesner

Publication for Complex heatmaps

Complex heatmaps citations


Machine learning based diagnosis for disseminated intravascular coagulation (DIC): Development, external validation, and comparison to scoring systems

PLoS One
PMCID: 5931474
PMID: 29718941
DOI: 10.1371/journal.pone.0195861

[…] []. JMHW and JAAM scores could not be evaluated in set 2 as FDP was lacked in the DIC profile of set 2.Statistics software R version 3.4.3 was used for data analysis. Datasets were visualized using ‘ComplexHeatmap’ package []. Performance evaluation was achieved via receiver operating characteristic (ROC) curve analysis, and calculation of AUC using the ‘pROC’ package []. The cut-off value (0.501 […]


Racial differences in endometrial cancer molecular portraits in The Cancer Genome Atlas

PMCID: 5908308
PMID: 29682207
DOI: 10.18632/oncotarget.24907

[…] ng customised functions to generate MA and volcano plots, and also inspection of Cook's distance and plots of mean of normalised counts versus p-value. Clustering with heatmap was performed using the ComplexHeatmap package [] and included all variance stabilised counts for differentially expressed transcripts at 5% FDR and log2FC>2. Prior to heatmap generation, partitioning around medoids (PAM) wa […]


Alpha oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A

Sci Rep
PMCID: 5852004
PMID: 29540744
DOI: 10.1038/s41598-018-22771-2
call_split See protocol

[…] IlluminaMethylationManifest, a class built within the minfi package. Volcano plots were constructed using the Biconductor package, TCGAbiolinks. Heatmaps were created using the Bioconductor package, ComplexHeatmap. Differentially methylated genes (DMGs) were identified using a simple T-test comparing treated and un-treated groups. Additionally, we compared the mean β-values of two groups and only […]


De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

PMCID: 5821079
PMID: 29463655
DOI: 10.1128/mBio.01650-17

[…] ere is a full list at Functional annotations for each isolate were compared (compare function) and summary heatmaps prepared from the parsed results using ComplexHeatmap (1.12.0) in R. Gene ontology (GO) terms were compared between isolates using goatools and Fisher’s exact test with false-discovery rate and multiple-test correction ( […]


Methylation profiling identifies two subclasses of squamous cell carcinoma related to distinct cells of origin

Nat Commun
PMCID: 5805678
PMID: 29422656
DOI: 10.1038/s41467-018-03025-1

[…] -house control data set (>2%, among 280 controls). Based on ANNOVAR annotations, only the variants in coding regions were selected for the analysis. The oncoprint plot was finally generated using the ComplexHeatmap R package. […]


Molecular characterization of metastatic pancreatic neuroendocrine tumors (PNETs) using whole genome and transcriptome sequencing

PMCID: 5793777
PMID: 29092957
DOI: 10.1101/mcs.a002329

[…] LOH events and CNAs were illustrated using the Bioconductor package GenVisR (). Heatmaps were generated using the Bioconductor package ComplexHeatmap () and R package gplots. […]


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Complex heatmaps institution(s)
Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
Complex heatmaps funding source(s)
This work was supported by the German Cancer Research Center-Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and the BMBF-funded de.NBI HD-HuB network (#031A537A, #031A537C).

Complex heatmaps reviews

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Gyan Prakash Mishra

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I like this tool very much, gives beautiful and easy interpretable heatmap, you have got all the controls over this tool and can tweak everything in this tool.

yang ou

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