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scDesign3

This is the development version of scDesign3; for the stable release version, see scDesign3.

A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics


Bioconductor version: Development (3.19)

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]

Maintainer: Dongyuan Song <dongyuansong at ucla.edu>

Citation (from within R, enter citation("scDesign3")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scDesign3")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews GeneExpression, Sequencing, SingleCell, Software, Spatial
Version 1.1.2
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.3.0)
Imports dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, rvinecopulib, 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, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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