Simple Simulation of Single-cell RNA Sequencing Data


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Documentation for package ‘splatter’ version 1.0.3

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splatter-package splatter.
addFeatureStats Add feature statistics
addGeneLengths Add gene lengths
bridge Brownian bridge
compareSCESets Compare SCESet objects
diffSCESets Diff SCESet objects
expandParams Expand parameters
expandParams-method Expand parameters
getLNormFactors Get log-normal factors
getParam Get a parameter
getParam-method Get a parameter
getParams Get parameters
getPathOrder Get path order
listSims List simulations
logistic Logistic function
lun2Estimate Estimate Lun2 simulation parameters
lun2Estimate.matrix Estimate Lun2 simulation parameters
lun2Estimate.SCESet 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.SCESet Estimate Lun simulation parameters
LunParams The LunParams class
LunParams-class The LunParams class
lunSimulate Lun simulation
makeCompPanel Make comparison panel
makeDiffPanel Make difference panel
makeOverallPanel Make overall panel
newLun2Params New Params
newLunParams New Params
newParams New Params
newSCDDParams New Params
newSimpleParams New Params
newSplatParams New Params
Params The Params virtual class
Params-class The Params virtual class
rbindMatched Bind rows (matched)
scDDEstimate Estimate scDD simulation parameters
scDDEstimate.matrix Estimate scDD simulation parameters
scDDEstimate.SCESet 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.SCESet 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.SCESet 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
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 diffSCESets
winsorize Winsorize vector