| BEAM_res | This is a test data for this package test data describtion |
| cell_data_set | The cell_data_set class from https://github.com/cole-trapnell-lab/monocle3/blob/master/R/cell_data_set.R |
| cell_data_set-class | The cell_data_set class from https://github.com/cole-trapnell-lab/monocle3/blob/master/R/cell_data_set.R |
| check_dependency | Check and Install Required Packages |
| clusterData | Cluster Data Based on Different Methods |
| enrichCluster | Perform GO/KEGG Enrichment Analysis for Multiple Clusters |
| exprs | Generic to access cds count matrix |
| exprs-method | Method to access cds count matrix |
| exps | This is a test data for this package test data describtion |
| filter.std | using filter.std to filter low expression genes |
| filter.std modified by Mfuzz filter.std | using filter.std to filter low expression genes |
| getClusters | Determine Optimal Clusters for Gene Expression or Pseudotime Data |
| net | This is a test data for this package test data describtion |
| normalized_counts | Return a size-factor normalized and (optionally) log-transformed expression |
| plot_genes_branched_heatmap2 | Create a heatmap to demonstrate the bifurcation of gene expression along two branchs which is slightly modified in monocle2 |
| plot_multiple_branches_heatmap2 | Create a heatmap to demonstrate the bifurcation of gene expression along multiple branches |
| plot_pseudotime_heatmap2 | Plots a pseudotime-ordered, row-centered heatmap which is slightly modified in monocle2 |
| prepareDataFromscRNA | Prepare scRNA Data for clusterGvis Analysis |
| pre_pseudotime_matrix | Calculate and return a smoothed pseudotime matrix for the given gene list |
| pseudotime | Generic to extract pseudotime from CDS object |
| pseudotime-method | Method to extract pseudotime from CDS object |
| sig_gene_names | This is a test data for this package test data describtion |
| size_factors | Get the size factors from a cds object. |
| termanno | This is a test data for this package test data describtion |
| termanno2 | This is a test data for this package test data describtion |
| traverseTree | traverseTree function |
| visCluster | using visCluster to visualize cluster results from clusterData and enrichCluster output |