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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")):

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")
Overview of the tidySingleCellExperiment package HTML R Script
Reference Manual PDF

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) (3.5 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
System Requirements
URL https://github.com/stemangiola/tidySingleCellExperiment
Bug Reports https://github.com/stemangiola/tidySingleCellExperiment/issues
See More
Suggests BiocStyle, testthat, knitr, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me CuratedAtlasQueryR, sccomp, spicyWorkflow
Links To Me
Build Report 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