tidySpatialExperiment

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

SpatialExperiment with tidy principles

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DOI: 10.18129/B9.bioc.tidySpatialExperiment

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0009-0001-6242-4269 , 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 "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

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

Version 1.7.1

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

License GPL (>= 3)

Depends R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment, ttservice

Imports SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr, ggplot2 (>= 4.0.0), plotly, rlang, purrr, stringr, vctrs, tidyselect, pillar, cli, fansi, lifecycle, magick, tidygate (>= 1.0.13), shiny

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, scater, igraph, cowplot, DropletUtils, tidySummarizedExperiment

Linking To

Enhances

Depends On Me

Imports Me tidyomics

Suggests Me

Links To Me

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Package Archives

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

Source Package tidySpatialExperiment_1.7.1.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) tidySpatialExperiment_1.7.1.tgz

macOS Binary (arm64) tidySpatialExperiment_1.7.1.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/

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