Simple Simulation of Single-cell RNA Sequencing Data


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Documentation for package ‘splatter’ version 1.32.0

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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