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spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Bioconductor version: Release (3.19)

Inspect interactively the spatially-resolved transcriptomics data from the 10x Genomics Visium platform as well as data from the Maynard, Collado-Torres et al, Nature Neuroscience, 2021 project analyzed by Lieber Institute for Brain Development (LIBD) researchers and collaborators.

Author: Leonardo Collado-Torres [aut, cre] , Kristen R. Maynard [ctb] , Andrew E. Jaffe [ctb] , Brenda Pardo [ctb] , Abby Spangler [ctb] , Jesús Vélez Santiago [ctb] , Lukas M. Weber [ctb] , Louise Huuki-Myers [ctb] , Nicholas Eagles [ctb]

Maintainer: Leonardo Collado-Torres <lcolladotor at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Guide to Multi-Gene Plots HTML R Script
Guide to Spatial Registration HTML R Script
Introduction to spatialLIBD HTML R Script
Using spatialLIBD with 10x Genomics public datasets HTML R Script
Reference Manual PDF


biocViews ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, SpatialData, Tissue
Version 1.16.2
License Artistic-2.0
Depends SpatialExperiment(>= 1.3.3), R (>= 3.6)
Imports shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, fields, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble, rtracklayer, Matrix, BiocGenerics, GenomicRanges, magick, paletteer, scuttle, edgeR, limma, statmod, MatrixGenerics, rlang
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Suggests knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils
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Follow Installation instructions to use this package in your R session.

Source Package spatialLIBD_1.16.2.tar.gz
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