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Bioconductor - tidySpatialExperiment (development version)

tidySpatialExperiment

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

SpatialExperiment with tidy principles

Bioconductor version: Development (3.22)

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: 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 "4.5") 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")
Details biocViews GeneExpression, Infrastructure, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics Version 1.5.0 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License GPL (>= 3) Depends R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment Imports ttservice, SummarizedExperiment, SingleCellExperiment, BiocGenerics, Matrix, S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr, ggplot2, 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 See More Package Archives

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

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