spatialLIBD

DOI: 10.18129/B9.bioc.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 (3.13)

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]

Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML R Script Introduction to spatialLIBD
HTML R Script Using spatialLIBD with 10x Genomics public datasets
PDF   Reference Manual
Text   NEWS

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, Tissue
Version 1.3.19
License Artistic-2.0
Depends SpatialExperiment(>= 1.1.700), R (>= 3.6)
Imports shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, Polychrome, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, fields, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble
LinkingTo
Suggests knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, rtracklayer, pryr
SystemRequirements
Enhances
URL https://github.com/LieberInstitute/spatialLIBD
BugReports https://support.bioconductor.org/t/spatialLIBD
Depends On Me
Imports Me
Suggests Me BayesSpace
Links To Me
Build Report  

Package Archives

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

Source Package spatialLIBD_1.3.19.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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

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