aggregate_gene_expression	aggregate_gene_expression
align_cds	align_cds
calculateLW	calculateLW
calc_principal_graph	calc_principal_graph
cell_data_set	cell_data_set
cell_data_set-class	cell_data_set
cell_data_set-methods	cell_data_set-methods
choose_cells	choose_cells
choose_graph_segments	choose_graph_segments
clear_cds_slots	clear_cds_slots
clusters	clusters
clusters,cell_data_set-method	clusters-cell_data_set-method
cluster_cells	cluster_cells
coefficient_table	coefficient_table
combine_cds	combine_cds
compare_models	compare_models
detect_genes	detect_genes
estimate_size_factors	estimate_size_factors
evaluate_fits	evaluate_fits
exprs	exprs
exprs,cell_data_set-method	exprs-cell_data_set-method
fData	fData
fData,cell_data_set-method	fData-cell_data_set-method
fData<-	fData-set
fData<-,cell_data_set-method	fData-set-cell_data_set-method
find_gene_modules	find_gene_modules
find_nearest_vertex	find_nearest_vertex
fit_models	fit_models
fit_model_helper	fit_model_helper
generate_centers	generate_centers
generate_garnett_marker_file	generate_garnett_marker_file
get_citations	get_citations
get_genome_in_matrix_path	get_genome_in_matrix_path
graph_test	graph_test
learn_graph	learn_graph
load_a549	load_a549
load_cellranger_data	load_cellranger_data
load_mtx_data	load_mtx_data
load_worm_embryo	load_worm_embryo
mc_es_apply	mc_es_apply
model_predictions	model_predictions
my.aggregate.Matrix	my.aggregate.Matrix
new_cell_data_set	new_cell_data_set
normalized_counts	normalized_counts
order_cells	order_cells
partitions	partitions
partitions,cell_data_set-method	partitions-cell_data_set-method
pData	pData
pData,cell_data_set-method	pData-cell_data_set-method
pData<-	pData-set
pData<-,cell_data_set-method	pData-set-cell_data_set-method
plot_cells	plot_cells
plot_cells_3d	plot_cells_3d
plot_genes_by_group	plot_genes_by_group
plot_genes_in_pseudotime	plot_genes_in_pseudotime
plot_genes_violin	plot_genes_violin
plot_pc_variance_explained	plot_pc_variance_explained
plot_percent_cells_positive	plot_percent_cells_positive
preprocess_cds	preprocess_cds
principal_graph	principal_graph
principal_graph,cell_data_set-method	principal_graph-cell_data_set-method
principal_graph<-	principal_graph-set
principal_graph<-,cell_data_set-method	principal_graph-set-cell_data_set-method
principal_graph_aux	principal_graph_aux
principal_graph_aux,cell_data_set-method	principal_graph_aux-cell_data_set-method
principal_graph_aux<-	principal_graph_aux-set
principal_graph_aux<-,cell_data_set-method	principal_graph_aux-set-cell_data_set-method
pseudotime	pseudotime
pseudotime,cell_data_set-method	pseudotime-cell_data_set-method
reduce_dimension	reduce_dimension
repmat	repmat
size_factors	size_factors
size_factors<-	size_factors-set
soft_assignment	soft_assignment
sparse_prcomp_irlba	sparse_prcomp_irlba
top_markers	top_markers
