DPT                     Diffusion Pseudo Time
DPT matrix methods      DPT Matrix methods
DPT methods             DPT methods
DiffusionMap accessors
                        DiffusionMap accession methods
DiffusionMap class      Create a diffusion map of cells
DiffusionMap methods    DiffusionMap methods
ExpressionSet helpers   Convert object to ExpressionSet or read it from
                        a file
Gene Relevance          Gene relevances for entire data set
Gene Relevance plotting
                        Plot gene relevance or gradient map
Sigmas class            Sigmas Object
coercions               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
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 ARPACK
extractions             Extraction methods
find_dm_k               Find a suitable k
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
projection_dist         Projection distance
random_root             Find a random root cell index
updateObject-method     Update old DiffusionMaps or Sigmas to a newer
                        version
