spatialHeatmap

DOI: 10.18129/B9.bioc.spatialHeatmap  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see spatialHeatmap.

spatialHeatmap

Bioconductor version: 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>

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")

 

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

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