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spatialLIBD

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

Bioconductor version: Release (3.17)

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 "4.3") and enter: 

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

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")
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 1.12.0
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
Linking To
Suggests knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr
System Requirements
Enhances
URL https://github.com/LieberInstitute/spatialLIBD
Bug Reports https://support.bioconductor.org/tag/spatialLIBD
See More
Depends On Me
Imports Me escheR
Suggests Me BayesSpace, DESpace
Links To Me
Build Report  

Package Archives

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

Source Package spatialLIBD_1.12.0.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/
Package Downloads Report Download Stats