DOI: 10.18129/B9.bioc.spatialHeatmap  


Bioconductor version: Release (3.18)

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], Le Zhang [aut], Jordan Hayes [aut], Brendan Gongol [aut], Alexander Borowsky [aut], Julia Bailey-Serres [aut], Thomas Girke [aut]

Maintainer: Jianhai Zhang <jzhan067 at>

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


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HTML R Script (A) Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
HTML R Script (B) Co-visualizing Bulk and Single-cell Assay Data
HTML R Script (C) Creating Custom Annotated SVGs
PDF   Reference Manual
Text   NEWS


biocViews ATACSeq, CellBasedAssays, CellBiology, Clustering, DNASeq, DataRepresentation, GeneExpression, GeneTarget, GraphAndNetwork, Microarray, Network, Sequencing, SingleCell, Software, Spatial, TissueMicroarray, Visualization
Version 2.8.1
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 (>=, tibble, utils, xml2
Suggests AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery,,, org.At.tair.db,,, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, yaml
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Source Package spatialHeatmap_2.8.1.tar.gz
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