A B C D E F G L N O P R S T U misc
| as.data.frame-method | Coercion methods |
| as.data.frame.DiffusionMap | Coercion methods |
| as.data.frame.DPT | Coercion methods |
| as.ExpressionSet | Convert object to ExpressionSet or read it from a file |
| as.ExpressionSet-method | Convert object to ExpressionSet or read it from a file |
| as.matrix-method | Coercion methods |
| as.matrix.DPT | Coercion methods |
| branch_divide | DPT methods |
| Coercion methods | Coercion methods |
| colorlegend | Color legend |
| cube_helix | Sequential color palette using the cube helix system |
| data:guo | Guo at al. mouse embryonic stem cell qPCR data |
| data:guo_norm | Guo at al. mouse embryonic stem cell qPCR data |
| dataset | destiny generics |
| dataset-method | DPT methods |
| dataset-method | DiffusionMap accession methods |
| dataset-method | Gene Relevance methods |
| dataset.DPT | DPT methods |
| dataset.GeneRelevance | Gene Relevance methods |
| dataset<- | destiny generics |
| dataset<--method | DPT methods |
| dataset<--method | DiffusionMap accession methods |
| dataset<--method | Gene Relevance methods |
| destiny | Create and plot diffusion maps |
| destiny generics | destiny generics |
| DiffusionMap | Create a diffusion map of cells |
| DiffusionMap accession methods | DiffusionMap accession methods |
| DiffusionMap methods | DiffusionMap methods |
| DiffusionMap-class | Create a diffusion map of cells |
| dim-method | DPT Matrix methods |
| dim.DPT | DPT Matrix methods |
| distance | destiny generics |
| distance-method | DiffusionMap accession methods |
| distance-method | Gene Relevance methods |
| distance<- | destiny generics |
| distance<--method | DiffusionMap accession methods |
| distance<--method | Gene Relevance methods |
| dm_predict | Predict new data points using an existing DiffusionMap. The resulting matrix can be used in the plot method for the DiffusionMap |
| DPT | Diffusion Pseudo Time |
| DPT matrix methods | DPT Matrix methods |
| DPT methods | DPT methods |
| DPT-class | Diffusion Pseudo Time |
| eigenvalues | destiny generics |
| eigenvalues-method | DiffusionMap accession methods |
| eigenvalues<- | destiny generics |
| eigenvalues<--method | DiffusionMap accession methods |
| eigenvectors | destiny generics |
| eigenvectors-method | DiffusionMap accession methods |
| eigenvectors<- | destiny generics |
| eigenvectors<--method | DiffusionMap accession methods |
| eig_decomp | Fast eigen decomposition using 'eigs' |
| ExpressionSet helper methods | Convert object to ExpressionSet or read it from a file |
| Extraction methods | Extraction methods |
| featureNames-method | Gene Relevance methods |
| featureNames.GeneRelevance | Gene Relevance methods |
| featureNames<--method | Gene Relevance methods |
| find_dm_k | Find a suitable k |
| find_knn | kNN search |
| find_sigmas | Calculate the average dimensionality for m different gaussian kernel widths (sigma). |
| find_tips | Find tips in a DiffusionMap object |
| fortify.DiffusionMap | Coercion methods |
| fortify.DPT | Coercion methods |
| Gene Relevance methods | Gene Relevance methods |
| Gene Relevance plotting | Plot gene relevance or differential map |
| GeneRelevance-class | Gene relevances for entire data set |
| gene_relevance | Gene relevances for entire data set |
| gene_relevance-method | Gene relevances for entire data set |
| guo | Guo at al. mouse embryonic stem cell qPCR data |
| guo_norm | Guo at al. mouse embryonic stem cell qPCR data |
| l_which | Logical which |
| names-method | Extraction methods |
| names.DiffusionMap | Extraction methods |
| names.DPT | Extraction methods |
| ncol-method | DPT Matrix methods |
| ncol.DPT | DPT Matrix methods |
| nrow-method | DPT Matrix methods |
| nrow.DPT | DPT Matrix methods |
| optimal_sigma | destiny generics |
| optimal_sigma-method | DiffusionMap accession methods |
| optimal_sigma-method | Sigmas Object |
| plot-method | Plot gene relevance or differential map |
| plot-method | Plot DPT |
| plot-method | 3D or 2D plot of diffusion map |
| plot-method | Plot Sigmas object |
| plot.DiffusionMap | 3D or 2D plot of diffusion map |
| plot.DPT | Plot DPT |
| plot.Sigmas | Plot Sigmas object |
| plot_differential_map | Plot gene relevance or differential map |
| plot_differential_map-method | Plot gene relevance or differential map |
| plot_gene_relevance | Plot gene relevance or differential map |
| plot_gene_relevance-method | Plot gene relevance or differential map |
| plot_gene_relevance_rank | Plot gene relevance or differential map |
| plot_gene_relevance_rank-method | Plot gene relevance or differential map |
| print-method | DiffusionMap methods |
| print-method | Gene Relevance methods |
| print-method | Sigmas Object |
| print.DiffusionMap | DiffusionMap methods |
| projection_dist | Projection distance |
| random_root | Find a random root cell index |
| read.ExpressionSet | Convert object to ExpressionSet or read it from a file |
| scale_color_cube_helix | Sequential color palette using the cube helix system |
| scale_colour_cube_helix | Sequential color palette using the cube helix system |
| scale_fill_cube_helix | Sequential color palette using the cube helix system |
| show-method | DiffusionMap methods |
| show-method | Gene Relevance methods |
| show-method | Sigmas Object |
| show.DiffusionMap | DiffusionMap methods |
| Sigmas | Sigmas Object |
| sigmas | destiny generics |
| Sigmas-class | Sigmas Object |
| sigmas-method | DiffusionMap accession methods |
| Sigmas-methods | Sigmas Object |
| sigmas<- | destiny generics |
| sigmas<--method | DiffusionMap accession methods |
| tips | DPT methods |
| updateObject methods | Update old destiny objects to a newer version. |
| updateObject-method | Update old destiny objects to a newer version. |
| updateObject.DiffusionMap | Update old destiny objects to a newer version. |
| updateObject.GeneRelevance | Update old destiny objects to a newer version. |
| updateObject.Sigmas | Update old destiny objects to a newer version. |
| $-method | Extraction methods |
| $.DiffusionMap | Extraction methods |
| $.DPT | Extraction methods |
| [-method | DPT Matrix methods |
| [.DPT | DPT Matrix methods |
| [[-method | DPT Matrix methods |
| [[-method | Extraction methods |
| [[.DiffusionMap | Extraction methods |
| [[.DPT | Extraction methods |