spatialLIBD

DOI: 10.18129/B9.bioc.spatialLIBD    

This is the development version of spatialLIBD; for the stable release version, see spatialLIBD.

LIBD Visium spatial transcriptomics human pilot data inspector

Bioconductor version: Development (3.13)

Inspect interactively the spatial transcriptomics 10x Genomics Visium data from Maynard, Collado-Torres et al, 2020 analyzed by Lieber Institute for Brain Development researchers and collaborators.

Author: Leonardo Collado-Torres <lcolladotor at gmail.com>, Kristen Maynard <Kristen.Maynard at libd.org>, R. Jaffe <andrew.jaffe at libd.org>, Andrew Pardo <bpardo at lcgej.unam.mx>, E. Collado-Torres <lcolladotor at gmail.com>, Brenda Maynard <Kristen.Maynard at libd.org>

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

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, Tissue
Version 1.3.10
License Artistic-2.0
Depends SpatialExperiment(>= 1.1.5), R (>= 3.6)
Imports shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, Polychrome, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, fields, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble
LinkingTo
Suggests knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager
SystemRequirements
Enhances
URL https://github.com/LieberInstitute/spatialLIBD
BugReports https://support.bioconductor.org/t/spatialLIBD
Depends On Me
Imports Me
Suggests Me BayesSpace
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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/
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