spatialHeatmap
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see spatialHeatmap.
spatialHeatmap
Bioconductor version: 3.14
The spatialHeatmap package provides functionalities for visualizing cell-, tissue- and organ-specific data of biological assays by coloring the corresponding spatial features defined in anatomical images according to a numeric color key.
Author: Jianhai Zhang [aut, trl, cre], Jordan Hayes [aut], Le Zhang [aut], Bing Yang [aut], Wolf Frommer [aut], Julia Bailey-Serres [aut], Thomas Girke [aut]
Maintainer: Jianhai Zhang <jianhai.zhang at email.ucr.edu>
citation("spatialHeatmap")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spatialHeatmap")
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("spatialHeatmap")| spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Network Graphs | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, CellBasedAssays, CellBiology, Clustering, DNASeq, DataRepresentation, GeneExpression, GeneTarget, GraphAndNetwork, Microarray, Network, Sequencing, SingleCell, Software, TissueMicroarray, Visualization |
| Version | 2.0.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0) |
| Imports | av, BiocFileCache, data.table, DESeq2, distinct, edgeR, WGCNA, flashClust, htmlwidgets, genefilter, ggplot2, ggdendro, grImport, grid, gridExtra, gplots, igraph, HDF5Array, limma, methods, magick, rsvg, shiny, dynamicTreeCut, grDevices, graphics, ggplotify, parallel, plotly, rols, rappdirs, reshape2, stats, SummarizedExperiment, shinydashboard, S4Vectors, utils, visNetwork, UpSetR, xml2, yaml |
| System Requirements | |
| URL | https://github.com/jianhaizhang/spatialHeatmap |
| Bug Reports | https://github.com/jianhaizhang/spatialHeatmap/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, BiocSingular, RUnit, BiocGenerics, ExpressionAtlas, DT, Biobase, GEOquery, shinyWidgets, shinyjs, htmltools, shinyBS, sortable, scater, scran |
| 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 | spatialHeatmap_2.0.0.tar.gz |
| Windows Binary | spatialHeatmap_2.0.0.zip |
| macOS 10.13 (High Sierra) | spatialHeatmap_2.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/spatialHeatmap |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spatialHeatmap |
| Bioc Package Browser | https://code.bioconductor.org/browse/spatialHeatmap/ |
| Package Short Url | https://bioconductor.org/packages/spatialHeatmap/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |