tidySingleCellExperiment
This is the development version of tidySingleCellExperiment; for the stable release version, see tidySingleCellExperiment.
Brings SingleCellExperiment to the Tidyverse
Bioconductor version: Development (3.21)
'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:
Maintainer: Stefano Mangiola <mangiolastefano at gmail.com>
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 |
Details
| biocViews | AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, SingleCell, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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.
| Source Package | tidySingleCellExperiment_1.17.0.tar.gz |
| Windows Binary (x86_64) | tidySingleCellExperiment_1.17.0.zip |
| macOS Binary (x86_64) | tidySingleCellExperiment_1.17.0.tgz |
| macOS Binary (arm64) | tidySingleCellExperiment_1.17.0.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 |