spatialLIBD

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

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

Bioconductor version: Release (3.23)

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")):

Leonardo Collado-Torres. spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data. doi:10.18129/B9.bioc.spatialLIBD, R package version 1.24.0, https://bioconductor.org/packages/spatialLIBD.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, SpatialData, Tissue
Version	1.24.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
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
Suggests Me	Banksy, BatchSVG, BayesSpace, DESpace, GSVA
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	spatialLIBD_1.24.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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