DOI: 10.18129/B9.bioc.tidySingleCellExperiment  

Brings SingleCellExperiment to the Tidyverse

Bioconductor version: Release (3.18)

'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).

Author: Stefano Mangiola [aut, cre]

Maintainer: Stefano Mangiola <mangiolastefano at gmail.com>

Citation (from within R, enter citation("tidySingleCellExperiment")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Overview of the tidySingleCellExperiment package
PDF   Reference Manual


biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, SingleCell, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL-3
Depends R (>= 4.3.0), SingleCellExperiment
Imports dplyr, tidyr, ttservice (>= 0.3.8), SummarizedExperiment, tibble, ggplot2, plotly, magrittr, rlang, purrr, pkgconfig, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, Matrix, stats
Suggests BiocStyle, testthat, knitr, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq
URL https://github.com/stemangiola/tidySingleCellExperiment
BugReports https://github.com/stemangiola/tidySingleCellExperiment/issues
Depends On Me
Imports Me
Suggests Me CuratedAtlasQueryR, sccomp
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package tidySingleCellExperiment_1.12.0.tar.gz
Windows Binary tidySingleCellExperiment_1.12.0.zip
macOS Binary (x86_64) tidySingleCellExperiment_1.12.0.tgz
macOS Binary (arm64) tidySingleCellExperiment_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tidySingleCellExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tidySingleCellExperiment
Bioc Package Browser https://code.bioconductor.org/browse/tidySingleCellExperiment/
Package Short Url https://bioconductor.org/packages/tidySingleCellExperiment/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: