tidySingleCellExperiment
Brings SingleCellExperiment to the Tidyverse
Bioconductor version: 3.24 · Package version: 1.23.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
'tidySingleCellExperiment' is an adapter that abstracts the 'SingleCellExperiment' container in the form of a 'tibble'. This allows *tidy* data manipulation, nesting, and plotting. For example, a 'tidySingleCellExperiment' is directly compatible with functions from 'tidyverse' packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tidySingleCellExperiment")Details
| Maintainer | Stefano Mangiola <mangiolastefano@gmail.com> |
| Author | Stefano Mangiola [aut, cre] (ORCID: <https://orcid.org/0000-0001-7474-836X>) |
| License | GPL-3 |
| URL | https://github.com/stemangiola/tidySingleCellExperiment |
| Bug Reports | https://github.com/stemangiola/tidySingleCellExperiment/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/tidySingleCellExperiment/ |
Citation
From within R, enter citation("tidySingleCellExperiment"):
Stefano Mangiola. tidySingleCellExperiment: Brings SingleCellExperiment to the Tidyverse. doi:10.18129/B9.bioc.tidySingleCellExperiment, R package version 1.23.0, https://bioconductor.org/packages/tidySingleCellExperiment.
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 | tidySingleCellExperiment_1.23.0.tar.gz |
| Windows binary (x86_64) | tidySingleCellExperiment_1.23.0.zip |
| macOS binary (arm64) | tidySingleCellExperiment_1.23.0.tgz |
| macOS binary (x86_64) | tidySingleCellExperiment_1.23.0.tgz |
Dependencies
Depends: R (>= 4.4.0), SingleCellExperiment, ttservice (>= 0.4.0)
Imports: dplyr, tidyr, SummarizedExperiment, tibble, ggplot2, magrittr, rlang, purrr, pkgconfig, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, Matrix, stats
Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, plotly, rbibutils, prettydoc
Reverse dependencies
Depends On Me (1): tidySpatialExperiment
Imports Me (1): tidyomics
Suggests Me (1): sccomp