Simple Simulation of Single-cell RNA Sequencing Data


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Documentation for package ‘splatter’ version 1.10.1

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

-- A --

addFeatureStats Add feature statistics
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
bridge Brownian bridge
bringItemsForward Bring items forward

-- C --

compareSCEs Compare SingleCellExperiment objects

-- D --

diffSCEs Diff SingleCellExperiment objects

-- E --

expandParams Expand parameters
expandParams-method Expand parameters

-- G --

getBetaStepProbs Get Beta step probabilities
getCounts Get counts
getLNormFactors Get log-normal factors
getParam Get a parameter
getParam-method Get a parameter
getParams Get parameters
getPathOrder Get path order

-- K --

kersplatEstBCV Estimate Kersplat BCV parameters
kersplatEstimate Estimate Kersplat simulation parameters
kersplatEstimate.matrix Estimate Kersplat simulation parameters
kersplatEstimate.SingleCellExperiment Estimate Kersplat simulation parameters
kersplatEstLib Estimate Kersplat library size parameters
kersplatEstMean Estimate Kersplat means
kersplatGenNetwork Generate Kersplat gene network
KersplatParams The KersplatParams class
KersplatParams-class The KersplatParams class
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

-- 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
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
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 --

sampleDensity Sample density
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
selectFit Select fit
setParam Set a parameter
setParam-method Set a parameter
setParams Set parameters
setParams-method Set parameters
setParamsUnchecked Set parameters UNCHECKED
setParamUnchecked Set a parameter UNCHECKED
setParamUnchecked-method Set a parameter UNCHECKED
showDFs Show data.frame
showPP Show pretty print
showValues Show values
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
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 diffSCEs
summariseKS Summarise KS
summariseStats Summarise statistics

-- T --

tidyStatSumm Tidy summarised statistics

-- 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