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")):
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("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-vignette | 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/scDesign3/ |
| Package Short Url | https://bioconductor.org/packages/scDesign3/ |
| Package Downloads Report | Download Stats |