tidySingleCellExperiment
This is the released version of tidySingleCellExperiment; for the devel version, see tidySingleCellExperiment.
Brings SingleCellExperiment to the Tidyverse
Bioconductor version: Release (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]
Maintainer: Stefano Mangiola <mangiolastefano at gmail.com>
citation("tidySingleCellExperiment")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 |
Details
| biocViews | AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, SingleCell, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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 |
See More
| 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, OMA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tidySingleCellExperiment_1.22.0.tar.gz |
| Windows Binary (x86_64) | tidySingleCellExperiment_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | tidySingleCellExperiment_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | tidySingleCellExperiment_1.22.0.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 |