spatialLIBD

This is the released version of spatialLIBD; for the devel version, see spatialLIBD.

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

Bioconductor version: Release (3.22)

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] ORCID: 0000-0003-2140-308X , Kristen R. Maynard [ctb] ORCID: 0000-0003-0031-8468 , Andrew E. Jaffe [ctb] ORCID: 0000-0001-6886-1454 , Brenda Pardo [ctb] ORCID: 0000-0001-8103-7136 , Abby Spangler [ctb] ORCID: 0000-0002-0028-9348 , Jesús Vélez Santiago [ctb] ORCID: 0000-0001-5128-3838 , Lukas M. Weber [ctb] ORCID: 0000-0002-3282-1730 , Louise Huuki-Myers [ctb] ORCID: 0000-0001-5148-3602 , Nicholas Eagles [ctb] ORCID: 0000-0002-9808-5254

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

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

Installation

To install this package, start R (version "4.5") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, SpatialData, Tissue
Version	1.21.6
License	Artistic-2.0
Depends	SpatialExperiment(>= 1.3.3), R (>= 4.1)
Imports	shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble, rtracklayer, Matrix, BiocGenerics, GenomicRanges, magick, paletteer, scuttle, edgeR, limma, statmod, MatrixGenerics, rlang, dplyr, ComplexHeatmap, circlize
System Requirements
URL	https://github.com/LieberInstitute/spatialLIBD
Bug Reports	https://support.bioconductor.org/tag/spatialLIBD

Suggests	knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils, RColorBrewer
Linking To
Enhances
Depends On Me
Imports Me	DeconvoBuddies, visiumStitched, OSTA
Suggests Me	Banksy, BatchSVG, 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_1.21.6.tar.gz
Windows Binary (x86_64)
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