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tidySpatialExperiment

This is the development version of tidySpatialExperiment; to use it, please install the devel version of Bioconductor.

Brings SpatialExperiment to the tidyverse


Bioconductor version: Development (3.19)

tidySpatialExperiment provides a bridge between the SpatialExperiment package and the tidyverse ecosystem. It creates an invisible layer that allows you to interact with a SpatialExperiment object as if it were a tibble; enabling the use of functions from dplyr, tidyr, ggplot2 and plotly. But, underneath, your data remains a SpatialExperiment object.

Author: William Hutchison [aut, cre] , Stefano Mangiola [aut]

Maintainer: William Hutchison <hutchison.w at wehi.edu.au>

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

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("tidySpatialExperiment")

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("tidySpatialExperiment")
Overview HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Infrastructure, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics
Version 0.99.20
In Bioconductor since BioC 3.19 (R-4.4)
License GPL-3
Depends R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment
Imports ttservice, SummarizedExperiment, SingleCellExperiment, BiocGenerics, Matrix, S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr, ggplot2, magrittr, rlang, purrr, stringr, vctrs, tidyselect, pillar, cli, fansi, lifecycle
System Requirements
URL https://github.com/william-hutchison/tidySpatialExperiment https://william-hutchison.github.io/tidySpatialExperiment/
Bug Reports https://github.com/william-hutchison/tidySpatialExperiment/issues
See More
Suggests BiocStyle, testthat, knitr, markdown, SingleCellSignalR, SingleR, scater, scran, igraph, GGally, celldex, dittoSeq, cowplot, DropletUtils, plotly, tidySummarizedExperiment
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 tidySpatialExperiment_0.99.20.tar.gz
Windows Binary tidySpatialExperiment_0.99.20.zip
macOS Binary (x86_64) tidySpatialExperiment_0.99.20.tgz
macOS Binary (arm64) tidySpatialExperiment_0.99.20.tgz
Source Repository git clone https://git.bioconductor.org/packages/tidySpatialExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tidySpatialExperiment
Bioc Package Browser https://code.bioconductor.org/browse/tidySpatialExperiment/
Package Short Url https://bioconductor.org/packages/tidySpatialExperiment/
Package Downloads Report Download Stats