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