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>

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/
Package Downloads Report	Download Stats