theislab/destiny
Creates diffusion maps

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Source code
52
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theislab/destiny: Creates diffusion maps
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API

API for theislab/destiny
Creates diffusion maps

Global functions
$,DPT-method Man page
$,DiffusionMap-method Man page
$.DPT Man page
$.DiffusionMap Man page
.onLoad Source code
Coercion methods Man page
DPT Man page Source code
DPT matrix methods Man page
DPT methods Man page
DPT-class Man page
DiffusionMap Man page Source code
DiffusionMap accession methods Man page
DiffusionMap methods Man page
DiffusionMap-class Man page
ExpressionSet helper methods Man page
Extraction methods Man page
Gene Relevance methods Man page
Gene Relevance plotting Man page
GeneRelevance-class Man page
Sigmas Man page
Sigmas-class Man page
Sigmas-methods Man page
[,DPT,index,index,logicalOrMissing-method Man page
[,DPT,index,missing,logicalOrMissing-method Man page
[,DPT,missing,index,logicalOrMissing-method Man page
[,DPT,missing,missing,logicalOrMissing-method Man page
[.DPT Man page
[[,DPT,character,missing-method Man page
[[,DPT,index,index-method Man page
[[,DiffusionMap,character,missing-method Man page
[[.DPT Man page
[[.DiffusionMap Man page
accumulated_transitions Source code
as.ExpressionSet Man page
as.ExpressionSet,data.frame-method Man page
as.Matrix.dist Source code
as.data.frame,DPT-method Man page
as.data.frame,DiffusionMap-method Man page
as.data.frame.DPT Man page
as.data.frame.DiffusionMap Man page
as.matrix,DPT-method Man page
as.matrix.DPT Man page
auto_branch Source code
average_path Source code
branch_divide Man page Source code
branchcut Source code
censoring Source code
censoring_impl Source code
char_fallback Source code
check_dpt Source code
colorlegend Man page Source code
continuous_colors Source code
cube_helix Man page Source code
cut_branches Source code
data:guo Man page
data:guo_norm Man page
dataset Man page
dataset,DPT-method Man page
dataset,DiffusionMap-method Man page
dataset,GeneRelevance-method Man page
dataset.DPT Man page
dataset.GeneRelevance Man page
dataset<- Man page
dataset<-,DPT-method Man page
dataset<-,DiffusionMap-method Man page
dataset<-,GeneRelevance-method Man page
dataset_extract_doublematrix Source code
dataset_get_feature Source code
dataset_n_features Source code
dataset_n_observations Source code
dataset_names Source code
dataset_to_df Source code
decomp_transitions Source code
destiny Man page
destiny generics Man page
destiny-package Man page
differential_map Source code
dim,DPT-method Man page
dim.DPT Man page
distance Man page
distance,DiffusionMap-method Man page
distance,GeneRelevance-method Man page
distance<- Man page
distance<-,DiffusionMap-method Man page
distance<-,GeneRelevance-method Man page
dm_predict Man page Source code
dpt_for_branch Source code
dummy_dpt Source code
eig_decomp Man page Source code
eigenvalues Man page
eigenvalues,DiffusionMap-method Man page
eigenvalues<- Man page
eigenvalues<-,DiffusionMap-method Man page
eigenvectors Man page
eigenvectors,DiffusionMap-method Man page
eigenvectors<- Man page
eigenvectors<-,DiffusionMap-method Man page
emptyplot Source code
featureNames,GeneRelevance-method Man page
featureNames.GeneRelevance Man page
featureNames<-,GeneRelevance,characterOrFactor-method Man page
find_dm_k Man page Source code
find_knn Man page Source code
find_sigmas Man page Source code
find_tips Man page Source code
flipped_dcs Source code
fortify.DPT Man page Source code
fortify.DiffusionMap Man page Source code
gene_relevance Man page
gene_relevance,DiffusionMap,missing-method Man page
gene_relevance,matrix,dMatrixOrMatrix-method Man page
get_coords Source code
get_dim_range Source code
get_explicit_col Source code
get_knn Source code
get_louvain_clusters Source code
get_norm_p Source code
get_pca Source code
get_plot_fn Source code
get_sigmas Source code
get_smoothing Source code
guo Man page
guo_norm Man page
hasattr Source code
idx_list_to_vec Source code
is_distmatrix Source code
kendall_finite_cor Source code
l_which Man page Source code
names,DPT-method Man page
names,DiffusionMap-method Man page
names.DPT Man page
names.DiffusionMap Man page
ncol,DPT-method Man page
ncol.DPT Man page
no_censoring Source code
nrow,DPT-method Man page
nrow.DPT Man page
optimal_sigma Man page
optimal_sigma,DiffusionMap-method Man page
optimal_sigma,Sigmas-method Man page
organize_branches Source code
pca_scores Source code
plot,DPT,missing-method Man page
plot,DPT,numeric-method Man page
plot,DiffusionMap,missing-method Man page
plot,DiffusionMap,numeric-method Man page
plot,GeneRelevance,character-method Man page
plot,GeneRelevance,missing-method Man page
plot,GeneRelevance,numeric-method Man page
plot,Sigmas,missing-method Man page
plot.DPT Man page Source code
plot.DiffusionMap Man page Source code
plot.Sigmas Man page
plot_differential_map Man page
plot_differential_map,DiffusionMap,missing-method Man page
plot_differential_map,GeneRelevance,missing-method Man page
plot_differential_map,matrix,matrix-method Man page
plot_differential_map_impl Source code
plot_gene_relevance Man page
plot_gene_relevance,DiffusionMap,missing-method Man page
plot_gene_relevance,GeneRelevance,missing-method Man page
plot_gene_relevance,matrix,matrix-method Man page
plot_gene_relevance_impl Source code
plot_gene_relevance_rank Man page
plot_gene_relevance_rank,DiffusionMap,missing-method Man page
plot_gene_relevance_rank,GeneRelevance,missing-method Man page
plot_gene_relevance_rank,matrix,matrix-method Man page
plot_gene_relevance_rank_impl Source code
pr_rankcor Source code
pr_rankcor_prefun Source code
predict_censoring Source code
predict_censoring_impl Source code
print,DiffusionMap-method Man page
print,GeneRelevance-method Man page
print,Sigmas-method Man page
print.DiffusionMap Man page
projection_dist Man page Source code
proxy_add_rankcor_simil Source code
random_root Man page Source code
rank_mat Source code
read.ExpressionSet Man page Source code
rescale_mat Source code
runs Source code
scale_color_cube_helix Man page
scale_colour_cube_helix Man page Source code
scale_cube_helix Source code
scale_fill_cube_helix Man page Source code
set_palette Source code
show,DiffusionMap-method Man page
show,GeneRelevance-method Man page
show,Sigmas-method Man page
show.DiffusionMap Man page
sigma_msg Source code
sigmas Man page
sigmas,DiffusionMap-method Man page
sigmas<- Man page
sigmas<-,DiffusionMap-method Man page
stopifnot_distmatrix Source code
stopifsmall Source code
symmetricise Source code
test_censoring Source code
theme_really_minimal Source code
tips Man page Source code
tipstats Source code
transition_probabilities Source code
updateObject methods Man page
updateObject,DiffusionMap-method Man page
updateObject,GeneRelevance-method Man page
updateObject,Sigmas-method Man page
updateObject.DiffusionMap Man page
updateObject.GeneRelevance Man page
updateObject.Sigmas Man page
update_slot_names Source code
validate_censoring Source code
verbose_timing Source code
theislab/destiny documentation built on Nov. 19, 2024, 5:43 a.m.

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