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 methods
                        Gene Relevance methods
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
knn                     kNN search
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 destiny objects to a newer version.
