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ggspavis

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

Visualization functions for spatially resolved transcriptomics data


Bioconductor version: Development (3.19)

Visualization functions for spatially resolved transcriptomics datasets stored in SpatialExperiment format. Includes functions to create several types of plots for data from from spot-based (e.g. 10x Genomics Visium) and molecule-based (e.g. seqFISH) technological platforms.

Author: Lukas M. Weber [aut, cre] , Helena L. Crowell [aut]

Maintainer: Lukas M. Weber <lukas.weber.edu at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ggspavis")

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("ggspavis")
ggspavis overview HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews SingleCell, Software, Spatial, Transcriptomics
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License MIT + file LICENSE
Depends ggplot2
Imports SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, methods, stats
System Requirements
URL https://github.com/lmweber/ggspavis
Bug Reports https://github.com/lmweber/ggspavis/issues
See More
Suggests BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me Banksy, HCATonsilData
Links To Me
Build Report Build Report

Package Archives

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

Source Package ggspavis_1.9.0.tar.gz
Windows Binary ggspavis_1.9.0.zip
macOS Binary (x86_64) ggspavis_1.9.0.tgz
macOS Binary (arm64) ggspavis_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ggspavis
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ggspavis
Bioc Package Browser https://code.bioconductor.org/browse/ggspavis/
Package Short Url https://bioconductor.org/packages/ggspavis/
Package Downloads Report Download Stats