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tidySingleCellExperiment
This is thereleased version of tidySingleCellExperiment; for the devel version, seetidySingleCellExperiment.
Brings SingleCellExperiment to the Tidyverse
Bioconductor version: Release (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("tidySingleCellExperiment")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("tidySingleCellExperiment")For older versions of R, please refer to the appropriateBioconductor 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 | 1.20.1 |
| 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,generics |
| 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,spicyWorkflow |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | tidySingleCellExperiment_1.20.1.tar.gz |
| Windows Binary (x86_64) | tidySingleCellExperiment_1.20.1.zip (64-bit only) |
| macOS Binary (x86_64) | tidySingleCellExperiment_1.20.1.tgz |
| macOS Binary (arm64) | tidySingleCellExperiment_1.20.1.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 |
| Old Source Packages for BioC 3.22 | Source Archive |