Man pages for YosefLab/ImpulseDE2
Differential expression analysis of longitudinal count data sets

append_strReportAppend string to strReport in ImpulseDE2Object
computeNormConstCompute a normalisation constant for each sample
computeSizeFactorsCompute a size factor for each sample
estimateImpulseParamCompute peak and valley impulse model parameter...
estimateSigmoidParamCompute up and down sigmoid model parameter initialisations...
evalImpulseCompute value of impulse function given parameters.
evalImpulse_compCompiled function: evalImpulse
evalLogLikImpulseCost function for impulse model
evalLogLikImpulse_compCompiled function: evalLogLikImpulse
evalLogLikMuCost function for constant model
evalLogLikMu_compCompiled function: evalLogLikMu
evalLogLikSigmoidCost function for sigmoidal model
evalLogLikSigmoid_compCompiled function: evalLogLikSigmoid
evalSigmoidCompute value of sigmoidal model given parameters.
evalSigmoid_compCompiled function: evalSigmoid
fitConstImpulseFits impulse and constant models to all genes on all samples...
fitConstImpulseGeneFit an impulse and constant model to a single gene
fitConstModelFit a constant model to data of a gene
fitImpulseModelFit an impulse model to data of a gene
fitModelsFits impulse and constant models to a timecourse dataset
fitSigmoidGeneFit a sigmoidal model to a single gene
fitSigmoidModelFit a sigmoidal model to data of a gene
fitSigmoidModelsFits sigmoidal models to all genes on all all samples of a...
get_accessorsImpulseDE2Object "get" accession functions
ImpulseDE2Object-classContainer class for ImpulseDE2 output
list_accessionList-like accessor methods for ImpulseDE2Object
plotGenesPlots the impulse fits and data
plotHeatmapPlot structured z-value heatmaps of differentially expressed...
processDataCheck and process input to runImpulseDE2()
runDEAnalysisPerform differential expression analysis and identification...
runDESeq2Wrapper function for running DESeq2
runImpulseDE2ImpulseDE2 wrapper
set_accessorsImpulseDE2Object "set" accession functions
simulateDataSetImpulseDE2Simulate a data set for ImpulseDE2
updateDEAnalysisUpdate dfImpulseDE2Results after sigmoids have been fit...
writeReportToFilePrint ImpulseDE2 report to .txt file
YosefLab/ImpulseDE2 documentation built on June 3, 2017, 9:53 a.m.