spatialHeatmap

DOI: 10.18129/B9.bioc.spatialHeatmap  

spatialHeatmap

Bioconductor version: Release (3.17)

The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data.

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>

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")

 

HTML	R Script	(A) Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
HTML	R Script	(B) Co-visualization of Bulk and Single-cell Data
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, CellBasedAssays, CellBiology, Clustering, DNASeq, DataRepresentation, GeneExpression, GeneTarget, GraphAndNetwork, Microarray, Network, Sequencing, SingleCell, Software, Spatial, TissueMicroarray, Visualization
Version	2.6.2
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, genefilter, ggplot2, grImport, grid, gridExtra, gplots, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, scater, scuttle, scran, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2
LinkingTo
Suggests	AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, distinct, dendextend, DT, dynamicTreeCut, flashClust, ggdendro, HDF5Array, htmltools, htmlwidgets, 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, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, yaml
SystemRequirements
Enhances
URL	https://github.com/jianhaizhang/spatialHeatmap
BugReports	https://github.com/jianhaizhang/spatialHeatmap/issues
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_2.6.2.tar.gz
Windows Binary	spatialHeatmap_2.6.2.zip
macOS Binary (x86_64)	spatialHeatmap_2.6.2.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
Old Source Packages for BioC 3.17	Source Archive