tidySpatialExperiment

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see tidySpatialExperiment.

Brings SpatialExperiment to the tidyverse

DOI: 10.18129/B9.bioc.tidySpatialExperiment

Bioconductor version: 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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, Infrastructure, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics

Version 1.0.0

In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)

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

Suggests BiocStyle, testthat, knitr, markdown, SingleCellSignalR, SingleR, scater, scran, igraph, GGally, celldex, dittoSeq, cowplot, DropletUtils, plotly, tidySummarizedExperiment

Linking To

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Package Archives

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

Source Package tidySpatialExperiment_1.0.0.tar.gz

Windows Binary (x86_64) tidySpatialExperiment_1.0.0.zip

macOS Binary (x86_64) tidySpatialExperiment_1.0.0.tgz

macOS Binary (arm64) tidySpatialExperiment_1.0.0.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

Old Source Packages for BioC 3.19 Source Archive