EnrichedHeatmap

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see EnrichedHeatmap.

Making Enriched Heatmaps

Bioconductor version: 3.18

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 [aut, cre]

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

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")

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 HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, GenomeAnnotation, Sequencing, Software, Visualization

Version 1.32.0

In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)

License MIT + file LICENSE

Depends R (>= 3.6.0), methods, grid, ComplexHeatmap(>= 2.11.0), GenomicRanges

Imports matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges

System Requirements

URL https://github.com/jokergoo/EnrichedHeatmap

Suggests testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer

Linking To Rcpp

Enhances

Depends On Me

Imports Me extraChIPs, profileplyr

Suggests Me ComplexHeatmap, epistack, InteractiveComplexHeatmap

Links To Me

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Package Archives

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

Source Package EnrichedHeatmap_1.32.0.tar.gz

Windows Binary EnrichedHeatmap_1.32.0.zip

macOS Binary (x86_64) EnrichedHeatmap_1.32.0.tgz

macOS Binary (arm64) EnrichedHeatmap_1.32.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/EnrichedHeatmap

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EnrichedHeatmap

Bioc Package Browser https://code.bioconductor.org/browse/EnrichedHeatmap/

Package Short Url https://bioconductor.org/packages/EnrichedHeatmap/

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