tidySpatialExperiment
This is the development version of tidySpatialExperiment; for the stable release version, see tidySpatialExperiment.
SpatialExperiment with tidy principles
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.9.0 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tidySpatialExperiment_1.9.0.tar.gz |
| Windows Binary (x86_64) | tidySpatialExperiment_1.9.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | tidySpatialExperiment_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | tidySpatialExperiment_1.9.0.tgz |
| 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 |