tidySpatialExperiment
This is the development version of tidySpatialExperiment; for the stable release version, see tidySpatialExperiment.
SpatialExperiment with tidy principles
Bioconductor version: Development (3.21)
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:
Maintainer: William Hutchison <hutchison.w at wehi.edu.au>
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")| Overview | HTML | R Script |
| Reference Manual |
Details
| biocViews | GeneExpression, Infrastructure, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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
| Suggests | BiocStyle, testthat, knitr, markdown, scater, igraph, cowplot, DropletUtils, tidySummarizedExperiment |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tidySpatialExperiment_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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/ |
| Package Downloads Report | Download Stats |