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Bioconductor - spatialLIBD (development version)

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 (3.22)

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")

# 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")
Details biocViews ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, SpatialData, Tissue Version 1.21.5 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 See More 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 Links To Me Build Report Build Report Package Archives

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

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