tidySingleCellExperiment

This is the development version of tidySingleCellExperiment; for the stable release version, see tidySingleCellExperiment.

Brings SingleCellExperiment to the Tidyverse

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DOI: 10.18129/B9.bioc.tidySingleCellExperiment

Bioconductor version: Development (3.23)

'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] ORCID iD ORCID: 0000-0001-7474-836X

Maintainer: Stefano Mangiola <mangiolastefano at gmail.com>

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")

Overview of the tidySingleCellExperiment package HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, SingleCell, Software

Version 1.21.0

In Bioconductor since BioC 3.12 (R-4.0) (5 years)

License GPL-3

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

System Requirements

URL https://github.com/stemangiola/tidySingleCellExperiment

Bug Reports https://github.com/stemangiola/tidySingleCellExperiment/issues

Suggests BiocStyle, testthat, knitr, markdown, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, plotly, rbibutils, prettydoc

Linking To

Enhances

Depends On Me tidySpatialExperiment

Imports Me tidyomics

Suggests Me CuratedAtlasQueryR, sccomp

Links To Me

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Package Archives

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

Source Package tidySingleCellExperiment_1.21.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) tidySingleCellExperiment_1.21.0.tgz

macOS Binary (arm64) tidySingleCellExperiment_1.21.0.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/

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