scDesign3
This is the released version of scDesign3; for the devel version, see scDesign3.
A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics
Bioconductor version: Release (3.23)
We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.
Author: Dongyuan Song [aut, cre] 
, Qingyang Wang [aut] , Chenxin Jiang [aut]
Maintainer: Dongyuan Song <dongyuansong at ucla.edu>
citation("scDesign3")):Dongyuan Song, Qingyang Wang, Chenxin Jiang. scDesign3: A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics. doi:10.18129/B9.bioc.scDesign3, R package version 1.10.0, https://bioconductor.org/packages/scDesign3.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scDesign3")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("scDesign3")| scDesign3 Quickstart | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Sequencing, SingleCell, Software, Spatial |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop |
| System Requirements | |
| URL | https://github.com/SONGDONGYUAN1994/scDesign3 |
| Bug Reports | https://github.com/SONGDONGYUAN1994/scDesign3/issues |
See More
| Suggests | mvnfast, igraph, rvinecopulib, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scDesign3_1.10.0.tar.gz |
| Windows Binary (x86_64) | scDesign3_1.10.0.zip |
| macOS Binary (big-sur-x86_64) | scDesign3_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | scDesign3_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scDesign3 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scDesign3 |
| Package Short Url | https://bioconductor.org/packages/scDesign3/ |
| Package Downloads Report | Download Stats |