destiny-package	destiny
$,DiffusionMap-method	extractions
$,DPT-method	extractions
$.DiffusionMap	extractions
$.DPT	extractions
as.data.frame,DiffusionMap-method	coercions
as.data.frame,DPT-method	coercions
as.data.frame.DiffusionMap	coercions
as.data.frame.DPT	coercions
as.ExpressionSet	ExpressionSet-helpers
as.ExpressionSet,data.frame-method	ExpressionSet-helpers
as.matrix,DPT-method	coercions
as.matrix.DPT	coercions
branch_divide	DPT-methods
Coercion methods	coercions
colorlegend	colorlegend
cube_helix	cube_helix
data:guo	guo
data:guo_norm	guo
dataset	destiny-generics
dataset,DiffusionMap-method	DiffusionMap-accessors
dataset,DPT-method	DPT-methods
dataset,GeneRelevance-method	Gene-Relevance-methods
dataset.DPT	DPT-methods
dataset.GeneRelevance	Gene-Relevance-methods
dataset<-	destiny-generics
dataset<-,DiffusionMap-method	DiffusionMap-accessors
dataset<-,DPT-method	DPT-methods
dataset<-,GeneRelevance-method	Gene-Relevance-methods
destiny	destiny
destiny generics	destiny-generics
DiffusionMap	DiffusionMap-class
DiffusionMap accession methods	DiffusionMap-accessors
DiffusionMap methods	DiffusionMap-methods
DiffusionMap-class	DiffusionMap-class
dim,DPT-method	DPT-matrix-methods
dim.DPT	DPT-matrix-methods
distance	destiny-generics
distance,DiffusionMap-method	DiffusionMap-accessors
distance,GeneRelevance-method	Gene-Relevance-methods
distance<-	destiny-generics
distance<-,DiffusionMap-method	DiffusionMap-accessors
distance<-,GeneRelevance-method	Gene-Relevance-methods
dm_predict	dm_predict
DPT	DPT
DPT matrix methods	DPT-matrix-methods
DPT methods	DPT-methods
DPT-class	DPT
eigenvalues	destiny-generics
eigenvalues,DiffusionMap-method	DiffusionMap-accessors
eigenvalues<-	destiny-generics
eigenvalues<-,DiffusionMap-method	DiffusionMap-accessors
eigenvectors	destiny-generics
eigenvectors,DiffusionMap-method	DiffusionMap-accessors
eigenvectors<-	destiny-generics
eigenvectors<-,DiffusionMap-method	DiffusionMap-accessors
eig_decomp	eig_decomp
ExpressionSet helper methods	ExpressionSet-helpers
Extraction methods	extractions
featureNames,GeneRelevance-method	Gene-Relevance-methods
featureNames.GeneRelevance	Gene-Relevance-methods
featureNames<-,GeneRelevance,characterOrFactor-method	Gene-Relevance-methods
find_dm_k	find_dm_k
find_knn	knn
find_sigmas	find_sigmas
find_tips	find_tips
fortify.DiffusionMap	coercions
fortify.DPT	coercions
Gene Relevance methods	Gene-Relevance-methods
Gene Relevance plotting	Gene-Relevance-plotting
GeneRelevance-class	Gene-Relevance
gene_relevance	Gene-Relevance
gene_relevance,DiffusionMap,missing-method	Gene-Relevance
gene_relevance,matrix,dMatrixOrMatrix-method	Gene-Relevance
guo	guo
guo_norm	guo
l_which	l_which
names,DiffusionMap-method	extractions
names,DPT-method	extractions
names.DiffusionMap	extractions
names.DPT	extractions
ncol,DPT-method	DPT-matrix-methods
ncol.DPT	DPT-matrix-methods
nrow,DPT-method	DPT-matrix-methods
nrow.DPT	DPT-matrix-methods
optimal_sigma	destiny-generics
optimal_sigma,DiffusionMap-method	DiffusionMap-accessors
optimal_sigma,Sigmas-method	Sigmas-class
plot,DiffusionMap,missing-method	plot.DiffusionMap
plot,DiffusionMap,numeric-method	plot.DiffusionMap
plot,DPT,missing-method	plot.DPT
plot,DPT,numeric-method	plot.DPT
plot,GeneRelevance,character-method	Gene-Relevance-plotting
plot,GeneRelevance,missing-method	Gene-Relevance-plotting
plot,GeneRelevance,numeric-method	Gene-Relevance-plotting
plot,Sigmas,missing-method	plot.Sigmas
plot.DiffusionMap	plot.DiffusionMap
plot.DPT	plot.DPT
plot.Sigmas	plot.Sigmas
plot_differential_map	Gene-Relevance-plotting
plot_differential_map,DiffusionMap,missing-method	Gene-Relevance-plotting
plot_differential_map,GeneRelevance,missing-method	Gene-Relevance-plotting
plot_differential_map,matrix,matrix-method	Gene-Relevance-plotting
plot_gene_relevance	Gene-Relevance-plotting
plot_gene_relevance,DiffusionMap,missing-method	Gene-Relevance-plotting
plot_gene_relevance,GeneRelevance,missing-method	Gene-Relevance-plotting
plot_gene_relevance,matrix,matrix-method	Gene-Relevance-plotting
plot_gene_relevance_rank	Gene-Relevance-plotting
plot_gene_relevance_rank,DiffusionMap,missing-method	Gene-Relevance-plotting
plot_gene_relevance_rank,GeneRelevance,missing-method	Gene-Relevance-plotting
plot_gene_relevance_rank,matrix,matrix-method	Gene-Relevance-plotting
print,DiffusionMap-method	DiffusionMap-methods
print,GeneRelevance-method	Gene-Relevance-methods
print,Sigmas-method	Sigmas-class
print.DiffusionMap	DiffusionMap-methods
projection_dist	projection_dist
random_root	random_root
read.ExpressionSet	ExpressionSet-helpers
scale_color_cube_helix	cube_helix
scale_colour_cube_helix	cube_helix
scale_fill_cube_helix	cube_helix
show,DiffusionMap-method	DiffusionMap-methods
show,GeneRelevance-method	Gene-Relevance-methods
show,Sigmas-method	Sigmas-class
show.DiffusionMap	DiffusionMap-methods
Sigmas	Sigmas-class
sigmas	destiny-generics
sigmas,DiffusionMap-method	DiffusionMap-accessors
Sigmas-class	Sigmas-class
Sigmas-methods	Sigmas-class
sigmas<-	destiny-generics
sigmas<-,DiffusionMap-method	DiffusionMap-accessors
tips	DPT-methods
updateObject methods	updateObject-methods
updateObject,DiffusionMap-method	updateObject-methods
updateObject,GeneRelevance-method	updateObject-methods
updateObject,Sigmas-method	updateObject-methods
updateObject.DiffusionMap	updateObject-methods
updateObject.GeneRelevance	updateObject-methods
updateObject.Sigmas	updateObject-methods
[,DPT,index,index,logicalOrMissing-method	DPT-matrix-methods
[,DPT,index,missing,logicalOrMissing-method	DPT-matrix-methods
[,DPT,missing,index,logicalOrMissing-method	DPT-matrix-methods
[,DPT,missing,missing,logicalOrMissing-method	DPT-matrix-methods
[.DPT	DPT-matrix-methods
[[,DiffusionMap,character,missing-method	extractions
[[,DPT,character,missing-method	extractions
[[,DPT,index,index-method	DPT-matrix-methods
[[.DiffusionMap	extractions
[[.DPT	extractions
