trajectory-based differential expression analysis for sequencing data

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Documentation for package ‘tradeSeq’ version 1.18.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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.
conditionTest	Assess differential expression patterns between conditions within a lineage.
conditionTest-method	Assess differential expression patterns between conditions within a lineage.
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.
plotGeneCount-method	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
plot_evalutateK_results	Evaluate an appropriate number of knots.
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