tidySpatialExperiment
SpatialExperiment with tidy principles
Bioconductor version: 3.23 · Package version: 1.8.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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
| Maintainer | William Hutchison <hutchison.w@wehi.edu.au> |
| Author | William Hutchison [aut, cre] (ORCID: <https://orcid.org/0009-0001-6242-4269>), Stefano Mangiola [aut] |
| License | GPL (>= 3) |
| URL | https://github.com/william-hutchison/tidySpatialExperiment, https://william-hutchison.github.io/tidySpatialExperiment/ |
| Bug Reports | https://github.com/william-hutchison/tidySpatialExperiment/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, Infrastructure, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/tidySpatialExperiment/ |
Citation
From within R, enter citation("tidySpatialExperiment"):
William Hutchison, Stefano Mangiola. tidySpatialExperiment: SpatialExperiment with tidy principles. doi:10.18129/B9.bioc.tidySpatialExperiment, R package version 1.8.0, https://bioconductor.org/packages/tidySpatialExperiment.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | tidySpatialExperiment_1.8.0.tar.gz |
| Windows binary (x86_64) | tidySpatialExperiment_1.8.0.zip |
| macOS binary (arm64) | tidySpatialExperiment_1.8.0.tgz |
| macOS binary (x86_64) | tidySpatialExperiment_1.8.0.tgz |
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