Man pages for statOmics/tradeSeq
trajectory-based differential expression analysis for sequencing data
| associationTest | Perform statistical test to check whether gene expression is... |
| cascade | Get expression peak cascade of genes along a lineage. |
| celltype | A vector defining cell types, used in the package vignette. |
| clusterExpressionPatterns | Cluster gene expression patterns. |
| conditionTest | Assess differential expression patterns between conditions... |
| 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... |
| earlyDETest | Perform test of early differences between lineages |
| evaluateK | Evaluate the optimal number of knots required for fitGAM. |
| fitGAM | 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 |
| patternTest | Assess differential expression pattern between lineages. |
| plot_evalutateK_results | Evaluate an appropriate number of knots. |
| plotGeneCount | Plot gene expression in reduced dimension. |
| plotSmoothers | Plot the log-transformed counts and the fitted values for a... |
| predictCells | predictCells |
| predictSmooth | predictSmooth |
| sds | A SlingshotDataset object, used in the package unit tests. |
| startVsEndTest | Perform statistical test to check for DE between starting... |
