EnrichedHeatmap

DOI: 10.18129/B9.bioc.EnrichedHeatmap    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see EnrichedHeatmap.

Making Enriched Heatmaps

Bioconductor version: 3.9

Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.

Author: Zuguang Gu

Maintainer: Zuguang Gu <z.gu at dkfz.de>

Citation (from within R, enter citation("EnrichedHeatmap")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EnrichedHeatmap")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("EnrichedHeatmap")

 

HTML R Script 1. Make Enriched Heatmaps
HTML R Script 2. Visualize Categorical Signals
HTML R Script 3. Compare row ordering methods
HTML R Script 4. Visualize Comprehensive Associations in Roadmap dataset
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Coverage, GenomeAnnotation, Sequencing, Software, Visualization
Version 1.14.0
In Bioconductor since BioC 3.2 (R-3.2) (4 years)
License MIT + file LICENSE
Depends R (>= 3.1.2), methods, grid, ComplexHeatmap(>= 1.99.0), GenomicRanges
Imports matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges
LinkingTo Rcpp
Suggests testthat (>= 0.3), knitr, markdown, genefilter, RColorBrewer
SystemRequirements
Enhances
URL https://github.com/jokergoo/EnrichedHeatmap
Depends On Me
Imports Me profileplyr
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package EnrichedHeatmap_1.14.0.tar.gz
Windows Binary EnrichedHeatmap_1.14.0.zip
Mac OS X 10.11 (El Capitan) EnrichedHeatmap_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/EnrichedHeatmap
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EnrichedHeatmap
Package Short Url https://bioconductor.org/packages/EnrichedHeatmap/
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