Package: scDesign3 1.3.0

Dongyuan Song

scDesign3: A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics

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.

Authors:Dongyuan Song [aut, cre], Qingyang Wang [aut]

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scDesign3.pdf |scDesign3.html✨
scDesign3/json (API)
NEWS

# Install 'scDesign3' in R:
install.packages('scDesign3', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/songdongyuan1994/scdesign3/issues

Datasets:
  • example_sce - A SingelCellExperiment object containing both cell type and pseudotime

On BioConductor:scDesign3-1.3.0(bioc 3.20)scDesign3-1.2.0(bioc 3.19)

bioconductor-package

13 exports 1.64 score 95 dependencies

Last updated 2 months agofrom:1d45f65cc3

Exports:baconstruct_dataextract_parafit_copulafit_marginalgagamlss.bagamlss.gaperform_lrtplot_reduceddimscdesign3simu_newsparse_cov

Dependencies:abindaskpassassertthatBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecoopcpp11crayoncurlDelayedArraydplyrfansifarverformatRfutile.loggerfutile.optionsgamlssgamlss.datagamlss.distgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtableherehttrIRangesirlbaisobandjsonlitekde1dlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmgcvmimemunsellmvtnormnlmeopensslpbmcapplypillarpkgconfigpngR6randtoolboxrappdirsRColorBrewerRcppRcppEigenRcppThreadRcppTOMLreticulaterlangrngWELLrprojrootRSpectrarvinecopulibS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraysparseMVNSummarizedExperimentsurvivalsystibbletidyselectUCSC.utilsumaputf8vctrsviridisviridisLitewdmwithrXVectorzlibbioc

scDesign3 Quickstart

Dongyuan Song, Qingyang Wang

Rendered fromscDesign3.Rmdusingknitr::rmarkdownon Jul 10 2024.

Last update: 2023-09-16
Started: 2022-07-04