Complex heatmaps protocols

View Complex heatmaps computational protocol

Complex heatmaps statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Heatmap generation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Complex heatmaps specifications

Information


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

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Matthias Schlesner <>

Publication for Complex heatmaps

Complex heatmaps in pipelines

 (8)
2018
PMCID: 5743717
PMID: 29290775
DOI: 10.7150/jca.21925

[…] table . for evaluating the pearson's correlation coefficient between egfr and ieg expressions, tcga rna-seq data with egf mrna expressions above average was subjected to analysis and visualized by complexheatmap package in r. kaplan-meier (km) survival curve analysis and cox proportional hazards analysis were performed and visualized using survminer and survival package in r. biopsy samples […]

2018
PMCID: 5783949
PMID: 29367672
DOI: 10.1038/s41467-017-02107-w

[…] or dge-seq sample was projected on the first component of the 3 pca, and the first component coordinates were used to generate the three-dimension graph., heatmaps were drawn with the library complexheatmap with z-score of expression. cluster trees were computed with pvclust with correlation method as distance calculation and ward criteria as construction method., for expression profile […]

2018
PMCID: 5908308
PMID: 29682207
DOI: 10.18632/oncotarget.24907

[…] 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 […]

2018
PMCID: 5908308
PMID: 29682207
DOI: 10.18632/oncotarget.24907

[…] of each region was performed using genomicranges. for caucasians, we selected a pam cluster solution of five; for boaas, we selected four. clustering and heatmap generation was performed using the complexheatmap package []. dendrograms were generated using euclidean distance and ward's linkage. these groupings were then aligned with the 4 ec categories identified by the tcga [] by calculating […]

2017
PMCID: 5438707
PMID: 28423671
DOI: 10.18632/oncotarget.15993

[…] down-regulated in pc samples compared to normal samples ()., we used log2 transformed expected counts data of degs for clustering using ward's distance measure for hierarchical clustering using the complexheatmap package. we observed two major clusters, but these clusters are not as sharply distinguishable as dna methylation clusters (). we also did enrichment analysis of degs using webgestalt […]


To access a full list of citations, you will need to upgrade to our premium service.

Complex heatmaps in publications

 (52)
PMCID: 5908308
PMID: 29682207
DOI: 10.18632/oncotarget.24907

[…] 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 […]

PMCID: 5852004
PMID: 29540744
DOI: 10.1038/s41598-018-22771-2

[…] 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 […]

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

[…] is a full list at https://github.com/nextgenusfs/funannotate). 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 […]

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

[…] 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., infinium methylationepic beadchip data are available from the arrayexpress database under the accession number e-mtab-5738. whole-exome sequencing data has been deposited […]

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

[…] targets of drugs mentioned in this study were retrieved from ., loh events and cnas were illustrated using the bioconductor package genvisr (). heatmaps were generated using the bioconductor package complexheatmap () and r package gplots., dna and rna sequencing data have been deposited in the european genome-phenome archive (ega) as part of the study egas00001001159, accession ids […]


To access a full list of publications, you will need to upgrade to our premium service.

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

 (2)
star_border star_border star_border star_border star_border
star star star star star

Gyan Prakash Mishra

star_border star_border star_border star_border star_border
star star star star star
Desktop
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

star_border star_border star_border star_border star_border
star star star star star
Desktop
good