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spatialLIBD

This is the development version of spatialLIBD; for the stable release version, see spatialLIBD.

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


Bioconductor version: Development (3.20)

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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("spatialLIBD")

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("spatialLIBD")
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
NEWS Text

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, SpatialData, Tissue
Version 1.17.2
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
System Requirements
URL https://github.com/LieberInstitute/spatialLIBD
Bug Reports https://support.bioconductor.org/tag/spatialLIBD
See More
Suggests knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me Banksy, BayesSpace, DESpace
Links To Me
Build Report Build Report

Package Archives

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

Source Package spatialLIBD_1.17.2.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/spatialLIBD
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spatialLIBD
Package Short Url https://bioconductor.org/packages/spatialLIBD/
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