# trajectory-based differential expression analysis for sequencing data

## Documentation for package ‘tradeSeq’ version 1.12.0

- 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