scDesign3
This is thereleased version of scDesign3; for the devel version, seescDesign3.
A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0003-1114-1215, Qingyang Wang [aut] ORCID: 0000-0002-1051-609X, Chenxin Jiang [aut] ORCID: 0009-0005-7369-4116
Maintainer: Dongyuan Song <dongyuansong at ucla.edu>
citation("scDesign3")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("scDesign3")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("scDesign3")| scDesign3-quickstart-vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression,Sequencing,SingleCell,Software,Spatial |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 years) |
| License | MIT + fileLICENSE |
| 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 |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | scDesign3_1.8.0.tar.gz |
| Windows Binary (x86_64) | scDesign3_1.8.0.zip |
| macOS Binary (x86_64) | scDesign3_1.8.0.tgz |
| macOS Binary (arm64) | scDesign3_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scDesign3 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scDesign3 |
| Bioc Package Browser | https://code.bioconductor.org/browse/scDesign3/ |
| Package Short Url | https://bioconductor.org/packages/scDesign3/ |
| Package Downloads Report | Download Stats |