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Showing content from https://bioconductor.org/packages/devel/bioc/html/../../bioc/html/tidySingleCellExperiment.html below:

Bioconductor - tidySingleCellExperiment (development version)

tidySingleCellExperiment

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

Brings SingleCellExperiment to the Tidyverse

Bioconductor version: Development (3.22)

'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: 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 "4.5") 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 Details biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, SingleCell, Software Version 1.19.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License GPL-3 Depends R (>= 4.4.0), SingleCellExperiment Imports dplyr, tidyr, ttservice (>= 0.4.0), 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 See More Suggests BiocStyle, testthat, knitr, markdown, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, plotly Linking To Enhances Depends On Me tidySpatialExperiment Imports Me tidyomics 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.

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