tidySingleCellExperiment

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>

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("tidySingleCellExperiment")

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("tidySingleCellExperiment")

 

HTML	R Script	Overview of the tidySingleCellExperiment package
PDF		Reference Manual

Details

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
LinkingTo
Suggests	BiocStyle, testthat, knitr, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq
SystemRequirements
Enhances
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