| activation.fork | Estimate optimum of expression and time of activation |
| activation.statistics | Estimate optimum of expression and time of activation |
| activity.lasso | Predict regulatory impact (activity) of transcription factors |
| bootstrap.ppt | Sample pptree objects using bootstrap |
| branch.specific.genes | Assign genes differentially expressed between two... |
| classify.genes | Classify tree-associated genes |
| cleanup.branches | Remove spurious branches of pptree |
| corEvol | Estimate switch point in correlation trend |
| cor.mat | Calculate weighted pairwise correlations between columns of... |
| corMatrix | Estimates local gene-gene correlations in a sequence of... |
| corMatrixC | Estimates local gene-gene correlations in a sequence of... |
| crest | Processed neural crest single-cell data |
| decompose | Decompose a number by degrees of 2. |
| euclidean.mat | Calculate pairwise euclidean distances between columns of... |
| extract.subtree | Extract subtree of the tree |
| fig.cells | Visualize cells assigned to each local window |
| fig.cors | Visualize patterns of local correlations in consequtive... |
| fit.associated.genes | Model gene expression levels as a function of tree positions. |
| fit.ts | Model gene expression levels as a brancing spline function of... |
| fork.pt | Extract subtree of the tree |
| inclusion.stat | Show summary cumulative probability of genes inclusion in... |
| lambda.explore | Explore lambda |
| loc.opt | Identify all local optima for a time series data |
| matWVCorr | calculate weighted correlation between columns of a matrix... |
| mppt.tree | Sample pptree objects using different seeds |
| onset | Estimates inclusion times of genes in a correlated module for... |
| onset.est | Estimates inclusion times of genes in a correlated module |
| plotppt | Visualize pptree onto embedding |
| plotpptl | Visualize list of pptree objects onto embedding |
| ppt.tree | Reconstruction of the tree |
| project.cells.onto.ppt | Project cells onto the principal tree |
| setroot | Orient the tree by setting up the root |
| show.gene.inclusion | Show cumulative probability of gene inclusion in correlated... |
| show.inclusion.summary | Show summary cumulative probability of genes inclusion in... |
| sig.explore | Estimate optimal sigma parameter. |
| slide.cells | Assign cells in a probabilistic manner to non-intersecting... |
| slide.cors | Assign cells in a probabilistic manner to non-intersecting... |
| switchPoint | Estimates switch point in correlation trend |
| synchro | Estimates pseudotime trends of local intra- and inter-module... |
| synchro.path | Estimates pseudotime trends of local intra- and inter-module... |
| test.associated.genes | Determine a set of genes significantly associated with the... |
| test.fork.genes | Determine genes differentially upregulated after bifurcation... |
| visualise.clusters | Visualize clusters of genes using heatmap and consensus... |
| visualise.trajectory | Visualize branching trajectories of a particular gene. |
| visualize.synchro | Visualise local correlation trends of inter- and intra-... |
| wcr | calculate weighted correlation between columns of a matrix... |
