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spatialHeatmap

spatialHeatmap

Bioconductor version: Release (3.17)

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 <jzhan067 at ucr.edu>

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

Installation

To install this package, start R (version "4.3") 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")
Co-visualizing spatial heatmaps with single cell embedding plots HTML R Script
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Network Graphs HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, CellBasedAssays, CellBiology, Clustering, DNASeq, DataRepresentation, GeneExpression, GeneTarget, GraphAndNetwork, Microarray, Network, Sequencing, SingleCell, Software, Spatial, TissueMicroarray, Visualization
Version 2.6.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports data.table, dplyr, edgeR, WGCNA, flashClust, htmlwidgets, genefilter, ggplot2, ggdendro, grImport, grid, gridExtra, gplots, igraph, methods, Matrix, rsvg, shiny, dynamicTreeCut, grDevices, graphics, ggplotify, parallel, plotly, reshape2, scater, scuttle, scran, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, tibble, utils, visNetwork, UpSetR, xml2, yaml
Linking To
Suggests AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, distinct, dendextend, DT, HDF5Array, htmltools, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, rmarkdown, rols, rappdirs, RUnit, Rtsne, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, uwot
System Requirements
Enhances
URL https://github.com/jianhaizhang/spatialHeatmap
Bug Reports https://github.com/jianhaizhang/spatialHeatmap/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package spatialHeatmap_2.6.0.tar.gz
Windows Binary spatialHeatmap_2.6.0.zip
macOS Binary (x86_64) spatialHeatmap_2.6.0.tgz
macOS Binary (arm64) spatialHeatmap_2.6.0.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