spatialLIBD

DOI: 10.18129/B9.bioc.spatialLIBD  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see spatialLIBD.

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

Bioconductor version: 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>

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")

 

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, 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
LinkingTo
Suggests	knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr
SystemRequirements
Enhances
URL	https://github.com/LieberInstitute/spatialLIBD
BugReports	https://support.bioconductor.org/tag/spatialLIBD
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