BASiCSEstimate          Estimate BASiCS simulation parameters
BASiCSParams            The BASiCSParams class
BASiCSSimulate          BASiCS simulation
KersplatParams          The KersplatParams class
Lun2Params              The Lun2Params class
LunParams               The LunParams class
MFAParams               The MFAParams class
Params                  The Params virtual class
PhenoParams             The PhenoParams class
SCDDParams              The SCDDParams class
SimpleParams            The SimpleParams class
SparseDCParams          The SparseDCParams class
SplatParams             The SplatParams class
SplatPopParams          The SplatPopParams class
ZINBParams              The ZINBParams class
addFeatureStats         Add feature statistics
addGeneLengths          Add gene lengths
bridge                  Brownian bridge
bringItemsForward       Bring items forward
checkDependencies       Check dependencies
co.var                  Calculate coefficient of variation
compareSCEs             Compare SingleCellExperiment objects
diffSCEs                Diff SingleCellExperiment objects
expandParams            Expand parameters
getBetaStepProbs        Get Beta step probabilities
getCounts               Get counts
getLNormFactors         Get log-normal factors
getParam                Get a parameter
getParams               Get parameters
getPathOrder            Get path order
kersplatEstBCV          Estimate Kersplat BCV parameters
kersplatEstLib          Estimate Kersplat library size parameters
kersplatEstMean         Estimate Kersplat means
kersplatEstimate        Estimate Kersplat simulation parameters
kersplatGenNetwork      Generate Kersplat gene network
kersplatSample          Kersplat sample
kersplatSelectRegs      Select Kersplat regulators
kersplatSetup           Kersplat setup
kersplatSimAmbientCounts
                        Simulate Kersplat ambient counts
kersplatSimCellCounts   Simulate Kersplat cell counts
kersplatSimCellMeans    Simulate Kersplat cell means
kersplatSimCounts       Simulate Kersplat final counts
kersplatSimGeneMeans    Simulate Kersplat gene means
kersplatSimLibSizes     Simulate Kersplat library sizes
kersplatSimPaths        Simulate Kersplat paths
kersplatSimulate        Kersplat simulation
listSims                List simulations
logistic                Logistic function
lun2Estimate            Estimate Lun2 simulation parameters
lun2Simulate            Lun2 simulation
lunEstimate             Estimate Lun simulation parameters
lunSimulate             Lun simulation
makeCompPanel           Make comparison panel
makeDiffPanel           Make difference panel
makeOverallPanel        Make overall panel
mfaEstimate             Estimate mfa simulation parameters
mfaSimulate             MFA simulation
minimiseSCE             Minimise SCE
mockBulkMatrix          Generate mock bulk population scale expression
                        data
mockBulkeQTL            Generate mock eQTL mapping results
mockGFF                 Generate mock gff
mockVCF                 Generate mock vcf
newParams               New Params
phenoEstimate           Estimate PhenoPath simulation parameters
phenoSimulate           PhenoPath simulation
rbindMatched            Bind rows (matched)
sampleDensity           Sample density
scDDEstimate            Estimate scDD simulation parameters
scDDSimulate            scDD simulation
selectFit               Select fit
setParam                Set a parameter
setParamUnchecked       Set a parameter UNCHECKED
setParams               Set parameters
setParamsUnchecked      Set parameters UNCHECKED
showDFs                 Show data.frame
showPP                  Show pretty print
showValues              Show values
simpleEstimate          Estimate simple simulation parameters
simpleSimulate          Simple simulation
sparseDCEstimate        Estimate SparseDC simulation parameters
sparseDCSimulate        SparseDC simulation
sparsifyMatrices        Sparsify matrices
splatEstBCV             Estimate Splat Biological Coefficient of
                        Variation parameters
splatEstDropout         Estimate Splat dropout parameters
splatEstLib             Estimate Splat library size parameters
splatEstMean            Estimate Splat mean parameters
splatEstOutlier         Estimate Splat expression outlier parameters
splatEstimate           Estimate Splat simulation parameters
splatPopAssignMeans     Sample expression mean and variance for each
                        gene
splatPopCleanSCE        Clean up the population-scale SCE to remove
                        redundant information
splatPopEstimate        Estimate population/eQTL simulation parameters
splatPopEstimateEffectSize
                        Estimate eQTL Effect Size parameters
splatPopEstimateMeanCV
                        Estimate gene mean and gene mean variance
                        parameters
splatPopGroupEffects    Assign group-specific eQTL and DEGs.
splatPopParseGenes      Generate population key matrix from random or
                        gff provided gene information
splatPopParseVCF        Format and subset genotype data from a VCF
                        file.
splatPopQuantNorm       Quantile normalize by sample to fit sc
                        expression distribution.
splatPopQuantNormKey    Add quantile normalized gene mean and cv info
                        the eQTL key.
splatPopSimEffects      Add eQTL effects to means matrix
splatPopSimGeneMeans    Simulate gene means for splatPop
splatPopSimMeans        Simulate mean gene expression matrix without
                        eQTL effects
splatPopSimulate        splatPop simulation
splatPopSimulateMeans   splatPopSimulateMeans
splatPopSimulateSC      splatPopSimulateSC
splatPopSimulateSample
                        splatPopSimulateSample simulation
splatPopeQTLEffects     Assign eGenes-eSNPs pairs and effect sizes.
splatSimBCVMeans        Simulate BCV means
splatSimBatchCellMeans
                        Simulate batch means
splatSimBatchEffects    Simulate batch effects
splatSimCellMeans       Simulate cell means
splatSimDE              Simulate group differential expression
splatSimDropout         Simulate dropout
splatSimGeneMeans       Simulate gene means
splatSimLibSizes        Simulate library sizes
splatSimTrueCounts      Simulate true counts
splatSimulate           Splat simulation
splatter                splatter.
summariseDiff           Summarise diffSCEs
summariseKS             Summarise KS
summariseStats          Summarise statistics
tidyStatSumm            Tidy summarised statistics
winsorize               Winsorize vector
zinbEstimate            Estimate ZINB-WaVE simulation parameters
zinbSimulate            ZINB-WaVE simulation
