Coercion methods        Coercion methods
colorlegend             Color legend
cube_helix              Sequential color palette using the cube helix
                        system
destiny                 Create and plot diffusion maps
destiny generics        destiny generics
DiffusionMap accession methods
                        DiffusionMap accession methods
DiffusionMap methods    DiffusionMap methods
DiffusionMap-class      Create a diffusion map of cells
dm_predict              Predict new data points using an existing
                        DiffusionMap. The resulting matrix can be used
                        in the plot method for the DiffusionMap
DPT matrix methods      DPT Matrix methods
DPT methods             DPT methods
DPT-class               Diffusion Pseudo Time
eig_decomp              Fast eigen decomposition using 'eigs'
ExpressionSet helper methods
                        Convert object to ExpressionSet or read it from
                        a file
Extraction methods      Extraction 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
Gene Relevance methods
                        Gene Relevance methods
GeneRelevance-class     Gene relevances for entire data set
guo                     Guo at al. mouse embryonic stem cell qPCR data
l_which                 Logical which
plot_differential_map   Plot gene relevance or differential map
plot.DiffusionMap       3D or 2D plot of diffusion map
plot.DPT                Plot DPT
plot.Sigmas             Plot Sigmas object
projection_dist         Projection distance
random_root             Find a random root cell index
Sigmas-class            Sigmas Object
updateObject methods    Update old destiny objects to a newer version.
