EnrichedHeatmap
This is the development version of EnrichedHeatmap; for the stable release version, see EnrichedHeatmap.
Making Enriched Heatmaps
Bioconductor version: Development (3.24)
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.
Maintainer: Zuguang Gu <guzuguang at suat-sz.edu.cn>
citation("EnrichedHeatmap")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| The EnrichedHeatmap package | HTML |
| Reference Manual | |
| NEWS | Text |
| LICENSE | Text |
Details
| biocViews | Coverage, GenomeAnnotation, Sequencing, Software, Visualization |
| Version | 1.43.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0.0), 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 |
See More
| Suggests | testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | profileplyr |
| Suggests Me | ComplexHeatmap, epistack, extraChIPs, InteractiveComplexHeatmap |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EnrichedHeatmap_1.43.0.tar.gz |
| Windows Binary (x86_64) | EnrichedHeatmap_1.43.0.zip |
| macOS Binary (big-sur-x86_64) | EnrichedHeatmap_1.43.0.tgz |
| macOS Binary (sonoma-arm64) | EnrichedHeatmap_1.43.0.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/ |
| Package Downloads Report | Download Stats |