Simple Simulation of Single-cell RNA Sequencing Data

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Documentation for package ‘splatter’ version 1.2.1

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A B C D E G L M N P R S W Z

splatter-package splatter.

-- A --

addFeatureStats Add feature statistics
addGeneLengths Add gene lengths

-- B --

BASiCSEstimate Estimate BASiCS simulation parameters
BASiCSEstimate.matrix Estimate BASiCS simulation parameters
BASiCSEstimate.SCESet Estimate BASiCS simulation parameters
BASiCSParams The BASiCSParams class
BASiCSParams-class The BASiCSParams class
BASiCSSimulate BASiCS simulation
bridge Brownian bridge

-- C --

compareSCEs Compare SingleCellExperiment objects

-- D --

diffSCEs Diff SingleCellExperiment objects

-- E --

expandParams Expand parameters
expandParams-method Expand parameters

-- G --

getLNormFactors Get log-normal factors
getParam Get a parameter
getParam-method Get a parameter
getParams Get parameters
getPathOrder Get path order

-- L --

listSims List simulations
logistic Logistic function
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

-- N --

newBASiCSParams New Params
newLun2Params New Params
newLunParams New Params
newMFAParams New Params
newParams New Params
newPhenoParams New Params
newSCDDParams New Params
newSimpleParams New Params
newSplatParams 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

-- R --

rbindMatched Bind rows (matched)

-- 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
setParamsUnchecked Set parameters UNCHECKED
setParamUnchecked Set a parameter UNCHECKED
setParamUnchecked-method Set a parameter UNCHECKED
showPP Show pretty print
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
splatEstBCV Estimate Splat Biological Coefficient of Variation parameters
splatEstDropout Estimate Splat dropout parameters
splatEstimate Estimate Splat simulation parameters
splatEstimate.matrix Estimate Splat simulation parameters
splatEstimate.SingleCellExperiment Estimate Splat simulation parameters
splatEstLib Estimate Splat library size parameters
splatEstMean Estimate Splat mean parameters
splatEstOutlier Estimate Splat expression outlier parameters
SplatParams The SplatParams class
SplatParams-class The SplatParams class
splatSimBatchCellMeans Simulate batch means
splatSimBatchEffects Simulate batch effects
splatSimBCVMeans Simulate BCV means
splatSimCellMeans Simulate cell means
splatSimDE Simulate group differential expression
splatSimDropout Simulate dropout
splatSimGeneMeans Simulate gene means
splatSimGroupCellMeans Simulate cell means
splatSimGroupDE Simulate group differential expression
splatSimLibSizes Simulate library sizes
splatSimPathCellMeans Simulate cell means
splatSimPathDE Simulate group differential expression
splatSimSingleCellMeans Simulate cell means
splatSimTrueCounts Simulate true counts
splatSimulate Splat simulation
splatSimulateGroups Splat simulation
splatSimulatePaths Splat simulation
splatSimulateSingle Splat simulation
splatter splatter.
summariseDiff Summarise diffSCESs

-- W --

winsorize Winsorize vector

-- 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