# Simple Simulation of Single-cell RNA Sequencing Data

## Documentation for package ‘splatter’ version 1.35.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D G K L M N P S Z

## -- A --

addGeneLengths | Add gene lengths

## -- B --

BASiCSEstimate | Estimate BASiCS simulation parameters
BASiCSEstimate.matrix | Estimate BASiCS simulation parameters
BASiCSEstimate.SingleCellExperiment | Estimate BASiCS simulation parameters
BASiCSParams | The BASiCSParams class
BASiCSParams-class | The BASiCSParams class
BASiCSSimulate | BASiCS simulation

## -- C --

compareSCEs | Compare SingleCellExperiment objects

## -- D --

diffSCEs | Diff SingleCellExperiment objects

## -- G --

getParam | Get a parameter
getParam-method | Get a parameter
getParams | Get parameters

## -- K --

kersplatEstimate | Estimate Kersplat simulation parameters
kersplatEstimate.matrix | Estimate Kersplat simulation parameters
kersplatEstimate.SingleCellExperiment | Estimate Kersplat simulation parameters
KersplatParams | The KersplatParams class
KersplatParams-class | The KersplatParams class
kersplatSample | Kersplat sample
kersplatSetup | Kersplat setup
kersplatSimulate | Kersplat simulation

## -- L --

listSims | List simulations
lun2Estimate | Estimate Lun2 simulation parameters
lun2Estimate.matrix | Estimate Lun2 simulation parameters
lun2Estimate.SingleCellExperiment | Estimate Lun2 simulation parameters
Lun2Params | The Lun2Params class
Lun2Params-class | The Lun2Params class
lun2Simulate | Lun2 simulation
lunEstimate | Estimate Lun simulation parameters
lunEstimate.matrix | Estimate Lun simulation parameters
lunEstimate.SingleCellExperiment | Estimate Lun simulation parameters
LunParams | The LunParams class
LunParams-class | The LunParams class
lunSimulate | Lun simulation

## -- M --

makeCompPanel | Make comparison panel
makeDiffPanel | Make difference panel
makeOverallPanel | Make overall panel
mfaEstimate | Estimate mfa simulation parameters
mfaEstimate.matrix | Estimate mfa simulation parameters
mfaEstimate.SingleCellExperiment | Estimate mfa simulation parameters
MFAParams | The MFAParams class
MFAParams-class | The MFAParams class
mfaSimulate | MFA simulation
minimiseSCE | Minimise SCE
mockBulkeQTL | Generate mock eQTL mapping results
mockBulkMatrix | Generate mock bulk population scale expression data
mockEmpiricalSet | Generate set of "empirical" mock data
mockGFF | Generate mock gff
mockVCF | Generate mock vcf

## -- N --

newBASiCSParams | New Params
newKersplatParams | New Params
newLun2Params | New Params
newLunParams | New Params
newMFAParams | New Params
newParams | New Params
newPhenoParams | New Params
newSCDDParams | New Params
newSimpleParams | New Params
newSparseDCParams | New Params
newSplatParams | New Params
newSplatPopParams | New Params
newZINBParams | New Params

## -- P --

Params | The Params virtual class
Params-class | The Params virtual class
phenoEstimate | Estimate PhenoPath simulation parameters
phenoEstimate.matrix | Estimate PhenoPath simulation parameters
phenoEstimate.SingleCellExperiment | Estimate PhenoPath simulation parameters
PhenoParams | The PhenoParams class
PhenoParams-class | The PhenoParams class
phenoSimulate | PhenoPath simulation

## -- S --

scDDEstimate | Estimate scDD simulation parameters
scDDEstimate.default | Estimate scDD simulation parameters
scDDEstimate.matrix | Estimate scDD simulation parameters
scDDEstimate.SingleCellExperiment | Estimate scDD simulation parameters
SCDDParams | The SCDDParams class
SCDDParams-class | The SCDDParams class
scDDSimulate | scDD simulation
setParam | Set a parameter
setParam-method | Set a parameter
setParams | Set parameters
setParams-method | Set parameters
simpleEstimate | Estimate simple simulation parameters
simpleEstimate.matrix | Estimate simple simulation parameters
simpleEstimate.SingleCellExperiment | Estimate simple simulation parameters
SimpleParams | The SimpleParams class
SimpleParams-class | The SimpleParams class
simpleSimulate | Simple simulation
sparseDCEstimate | Estimate SparseDC simulation parameters
sparseDCEstimate.matrix | Estimate SparseDC simulation parameters
sparseDCEstimate.SingleCellExperiment | Estimate SparseDC simulation parameters
SparseDCParams | The SparseDCParams class
SparseDCParams-class | The SparseDCParams class
sparseDCSimulate | SparseDC simulation
splatEstimate | Estimate Splat simulation parameters
splatEstimate.matrix | Estimate Splat simulation parameters
splatEstimate.SingleCellExperiment | Estimate Splat simulation parameters
SplatParams | The SplatParams class
SplatParams-class | The SplatParams class
splatPopEstimate | Estimate population/eQTL simulation parameters
SplatPopParams | The SplatPopParams class
SplatPopParams-class | The SplatPopParams class
splatPopParseEmpirical | splatPopParseEmpirical
splatPopQuantNorm | Quantile normalize by sample to fit sc expression distribution.
splatPopSimulate | splatPop simulation
splatPopSimulateMeans | splatPopSimulateMeans
splatPopSimulateSC | splatPopSimulateSC
splatSimulate | Splat simulation
splatSimulateGroups | Splat simulation
splatSimulatePaths | Splat simulation
splatSimulateSingle | Splat simulation
summariseDiff | Summarise diffSCEs

## -- Z --

zinbEstimate | Estimate ZINB-WaVE simulation parameters
zinbEstimate.matrix | Estimate ZINB-WaVE simulation parameters
zinbEstimate.SingleCellExperiment | Estimate ZINB-WaVE simulation parameters
ZINBParams | The ZINBParams class
ZINBParams-class | The ZINBParams class
zinbSimulate | ZINB-WaVE simulation