tidySpatialExperiment
This is the released version of tidySpatialExperiment; for the devel version, see tidySpatialExperiment.
SpatialExperiment with tidy principles
Bioconductor version: Release (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] 
, Stefano Mangiola [aut]
Maintainer: William Hutchison <hutchison.w at wehi.edu.au>
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.
Installation
To install this package, start R (version "4.6") 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 |
Details
| biocViews | GeneExpression, Infrastructure, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 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 |
See More
| Suggests | BiocStyle, testthat, knitr, markdown, scater, igraph, cowplot, DropletUtils, tidySummarizedExperiment |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | tidyomics |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow 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 (big-sur-x86_64) | tidySpatialExperiment_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | tidySpatialExperiment_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tidySpatialExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tidySpatialExperiment |
| Package Short Url | https://bioconductor.org/packages/tidySpatialExperiment/ |
| Package Downloads Report | Download Stats |