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 (3.21)

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: ), Kristen R. Maynard [ctb] (ORCID: ), Andrew E. Jaffe [ctb] (ORCID: ), Brenda Pardo [ctb] (ORCID: ), Abby Spangler [ctb] (ORCID: ), Jesús Vélez Santiago [ctb] (ORCID: ), Lukas M. Weber [ctb] (ORCID: ), Louise Huuki-Myers [ctb] (ORCID: ), Nicholas Eagles [ctb] (ORCID: )

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


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	1.19.0
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, MatrixGenerics, rlang, dplyr
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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
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 [email protected]:packages/spatialLIBD
Package Short Url	https://bioconductor.org/packages/spatialLIBD/
Package Downloads Report	Download Stats