aggregate_gene_expression	aggregate_gene_expression
align_cds	align_cds
align_transform	align_transform
bpcells_prcomp_irlba	bpcells_prcomp_irlba
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
convert_counts_matrix	convert_counts_matrix
counts_row_order	counts_row_order
counts_row_order,cell_data_set-method	counts_row_order-cell_data_set-method
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
fit_models	fit_models
fix_missing_cell_labels	fix_missing_cell_labels
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
identity_table	identity_table
learn_graph	learn_graph
load_a549	load_a549
load_cellranger_data	load_cellranger_data
load_mm_data	load_mm_data
load_monocle_objects	load_monocle_objects
load_mtx_data	load_mtx_data
load_transform_models	load_transform_models
load_worm_embryo	load_worm_embryo
load_worm_l2	load_worm_l2
make_cds_nn_index	make_cds_nn_index
make_nn_index	make_nn_index
mc_es_apply	mc_es_apply
model_predictions	model_predictions
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_cells_per_sample_and_perturbation	plot_cells_per_sample_and_perturbation
plot_genes_by_group	plot_genes_by_group
plot_genes_hybrid	plot_genes_hybrid
plot_genes_in_pseudotime	plot_genes_in_pseudotime
plot_genes_violin	plot_genes_violin
plot_mito_umi_per_cell	plot_mito_umi_per_cell
plot_pc_variance_explained	plot_pc_variance_explained
plot_percent_cells_positive	plot_percent_cells_positive
plot_umi_per_cell	plot_umi_per_cell
plot_umi_per_cell_and_perturbation	plot_umi_per_cell_and_perturbation
preprocess_cds	preprocess_cds
preprocess_transform	preprocess_transform
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
reduce_dimension_transform	reduce_dimension_transform
repmat	repmat
save_monocle_objects	save_monocle_objects
save_transform_models	save_transform_models
search_cds_nn_index	search_cds_nn_index
search_nn_index	search_nn_index
search_nn_matrix	search_nn_matrix
set_cds_nn_index	set_cds_nn_index
set_cds_row_order_matrix	set_cds_row_order_matrix
set_matrix_control	set_matrix_control
set_nn_control	set_nn_control
size_factors	size_factors
size_factors<-	size_factors-set
soft_assignment	soft_assignment
sparse_prcomp_irlba	sparse_prcomp_irlba
top_markers	top_markers
transfer_cell_labels	transfer_cell_labels
