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. |
patternTest |
Assess differential expression pattern between lineages. |
patternTest-method |
Assess differential expression pattern between lineages. |
plotGeneCount |
Plot the gene in reduced dimension space |
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 |
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 |