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tidySpatialExperiment

SpatialExperiment with tidy principles

Bioconductor version: 3.23 · Package version: 1.8.0

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.

Installation

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

BiocManager::install("tidySpatialExperiment")

Details

MaintainerWilliam Hutchison <hutchison.w@wehi.edu.au>
AuthorWilliam Hutchison [aut, cre] (ORCID: <https://orcid.org/0009-0001-6242-4269>), Stefano Mangiola [aut]
LicenseGPL (>= 3)
URLhttps://github.com/william-hutchison/tidySpatialExperiment, https://william-hutchison.github.io/tidySpatialExperiment/
Bug Reportshttps://github.com/william-hutchison/tidySpatialExperiment/issues
Downloads rank250
Source branchRELEASE_3_23
biocViewsGeneExpression, Infrastructure, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics

Documentation

Download

Dependencies

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

Suggests: BiocStyle, testthat, knitr, markdown, scater, igraph, cowplot, DropletUtils, tidySummarizedExperiment

Reverse dependencies

Imports Me (1): tidyomics