List all the simulations that are currently available in Splatter with a brief description.
listSims(print = TRUE)
logical. Whether to print to the console. |
Invisibly returns a data.frame containing the information that is displayed.
listSims()#> Splatter currently contains 14 simulations #> #> Splat (splat) #> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter #> The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout and batch effects can be optionally added. #> #> Splat Single (splatSingle) #> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter #> The Splat simulation with a single population. #> #> Splat Groups (splatGroups) #> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter #> The Splat simulation with multiple groups. Each group can have it's own differential expression probability and fold change distribution. #> #> Splat Paths (splatPaths) #> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter #> The Splat simulation with differentiation paths. Each path can have it's own length, skew and probability. Genes can change in non-linear ways. #> #> Kersplat (kersplat) #> DOI: GitHub: Oshlack/splatter #> The Kersplat simulation extends the Splat model by adding a gene network, more complex cell structure, doublets and empty cells (Experimental). #> #> Simple (simple) #> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter #> A simple simulation with gamma means and negative binomial counts. #> #> Lun (lun) #> DOI: 10.1186/s13059-016-0947-7 GitHub: MarioniLab/Deconvolution2016 #> Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes. #> #> Lun 2 (lun2) #> DOI: 10.1093/biostatistics/kxw055 GitHub: MarioniLab/PlateEffects2016 #> Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used. #> #> scDD (scDD) #> DOI: 10.1186/s13059-016-1077-y GitHub: kdkorthauer/scDD #> The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions. #> #> BASiCS (BASiCS) #> DOI: 10.1371/journal.pcbi.1004333 GitHub: catavallejos/BASiCS #> The BASiCS simulation is based on a bayesian model used to deconvolve biological and technical variation and includes spike-ins and batch effects. #> #> mfa (mfa) #> DOI: 10.12688/wellcomeopenres.11087.1 GitHub: kieranrcampbell/mfa #> The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout. #> #> PhenoPath (pheno) #> DOI: 10.1101/159913 GitHub: kieranrcampbell/phenopath #> The PhenoPath simulation produces a pseudotime trajectory with different types of genes. #> #> ZINB-WaVE (zinb) #> DOI: 10.1101/125112 GitHub: drisso/zinbwave #> The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates. #> #> SparseDC (sparseDC) #> DOI: 10.1093/nar/gkx1113 GitHub: cran/SparseDC #> The SparseDC simulation simulates a set of clusters across two conditions, where some clusters may be present in only one condition. #>