spatialLIBD

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see spatialLIBD.

LIBD Visium spatial transcriptomics human pilot data inspector


Bioconductor version: 3.11

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 [aut, cre] , Kristen R. Maynard [ctb] , Andrew E. Jaffe [ctb]

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

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

Installation

To install this package, start R (version "4.0") 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")
Introduction to spatialLIBD HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, Tissue
Version 1.0.0
License Artistic-2.0
Depends SingleCellExperiment, 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
System Requirements
URL https://github.com/LieberInstitute/spatialLIBD
Bug Reports https://support.bioconductor.org/t/spatialLIBD
See More
Suggests knitr, rmarkdown, BiocStyle, knitcitations, testthat (>= 2.1.0), covr, here, BiocManager
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 spatialLIBD_1.0.0.tar.gz
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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