heatmaps
This is the released version of heatmaps; for the devel version, see heatmaps.
Flexible Heatmaps for Functional Genomics and Sequence Features
Bioconductor version: Release (3.23)
This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.
Author: Malcolm Perry <mgperry32 at gmail.com>
Maintainer: Malcolm Perry <mgperry32 at gmail.com>
citation("heatmaps")):
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")
BiocManager::install("heatmaps")
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("heatmaps")| Vignette Title | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FunctionalGenomics, SequenceMatching, Software, Visualization |
| Version | 1.36.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0) |
| Imports | methods, grDevices, graphics, stats, Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage, RColorBrewer, BiocGenerics, Seqinfo |
| System Requirements | |
| URL |
See More
| Suggests | BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | heatmaps_1.36.0.tar.gz |
| Windows Binary (x86_64) | heatmaps_1.36.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | heatmaps_1.36.0.tgz |
| macOS Binary (sonoma-arm64) | heatmaps_1.36.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/heatmaps |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/heatmaps |
| Bioc Package Browser | https://code.bioconductor.org/browse/heatmaps/ |
| Package Short Url | https://bioconductor.org/packages/heatmaps/ |
| Package Downloads Report | Download Stats |