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DESCRIPTION
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DESCRIPTION
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Package: scDesign3
Type: Package
Title: A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics
Version: 1.1.4
Authors@R:
c(person("Dongyuan", "Song", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-1114-1215")),
person("Qingyang", "Wang", , "[email protected]", role = c("aut"),
comment = c(ORCID = "0000-0002-1051-609X")),
person("Chenxin", "Jiang", , "[email protected]", role = c("aut"),
comment = c(ORCID = "0009-0005-7369-4116")))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
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
Suggests:
mvnfast,
igraph,
knitr,
rmarkdown,
testthat (>= 3.0.0),
RefManageR,
sessioninfo,
BiocStyle
biocViews:
Software,
SingleCell,
Sequencing,
GeneExpression,
Spatial
URL: https://github.com/SONGDONGYUAN1994/scDesign3
BugReports: https://github.com/SONGDONGYUAN1994/scDesign3/issues
RoxygenNote: 7.3.2
Config/testthat/edition: 3
VignetteBuilder: knitr