trajectory-based differential expression analysis for sequencing data

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Documentation for package ‘tradeSeq’ version 1.2.0

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associationTest Perform statistical test to check whether gene expression is constant across pseudotime within a lineage
associationTest-method Perform statistical test to check whether gene expression is constant across pseudotime within a lineage
celltype A vector defining cell types, used in the package vignette.
clusterExpressionPatterns Cluster gene expression patterns.
clusterExpressionPatterns-method Cluster gene expression patterns.
countMatrix A count matrix, used in the package vignette.
crv A SlingshotDataset object, used in the package vignette.
diffEndTest Perform statistical test to check for DE between final stages of every lineage.
diffEndTest-method Perform statistical test to check for DE between final stages of every lineage.
earlyDETest Perform test of early differences between lineages
earlyDETest-method Perform test of early differences between lineages
evaluateK Evaluate the optimal number of knots required for fitGAM.
evaluateK-method Evaluate the optimal number of knots required for fitGAM.
fitGAM fitGAM
fitGAM-method fitGAM
gamList A list of GAM models, used to demonstrate the various tests.
getSmootherPvalues Get smoother p-value as returned by 'mgcv'.
getSmootherTestStats Get smoother Chi-squared test statistics.
nknots knots
nknots-method knots
patternTest Assess differential expression pattern between lineages.
patternTest-method Assess differential expression pattern between lineages.
plotGeneCount Plot gene expression in reduced dimension.
plotSmoothers Plot the log-transformed counts and the fitted values for a particular gene along all lineages
plotSmoothers-method Plot the log-transformed counts and the fitted values for a particular gene along all lineages
predictCells predictCells
predictCells-method predictCells
predictSmooth predictSmooth
predictSmooth-method predictSmooth
sds A SlingshotDataset object, used in the package unit tests.
startVsEndTest Perform statistical test to check for DE between starting point and the end stages of every lineage
startVsEndTest-method Perform statistical test to check for DE between starting point and the end stages of every lineage