cole-trapnell-lab/monocle3
Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

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303
Source code
56
Man pages
101
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cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq
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API

API for cole-trapnell-lab/monocle3
Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Global functions
._._gc_matrix_object_remove_._. Source code
.onLoad Source code
`size_factors<-` Source code
add_citation Source code
aggregate_gene_expression Man page Source code
align_beta_transform Source code
align_cds Man page Source code
align_transform Man page Source code
bpcells_apply_transform Source code
bpcells_find_base_matrix Source code
bpcells_matdir_md5 Source code
bpcells_prcomp_irlba Man page Source code
branch_nodes Source code
cal_ncenter Source code
calc_principal_graph Man page Source code
calculateLW Source code
cell_data_set Man page
cell_data_set-class Man page
cell_data_set-methods Man page
check_bpcells_counts_matrix_pair Source code
check_cds_nn_index_is_current Source code
check_cds_nn_search_exists Source code
check_matrix_control Source code
check_monocle_object_files Source code
check_nn_col1 Source code
choose_cells Man page Source code
choose_graph_segments Man page Source code
clean_glmerMod_model_object Source code
clean_glmerMod_summary_object Source code
clean_mass_model_object Source code
clean_model_object Source code
clean_speedglm_model_object Source code
clean_vgam_model_object Source code
clean_zeroinfl_model_object Source code
clear_cds_nn_index Source code
clear_cds_slots Man page Source code
cluster_cells Man page Source code
cluster_cells_make_graph Source code
clusters Man page
clusters,cell_data_set-method Man page
coefficient_table Man page Source code
combine_cds Man page Source code
combine_cds_for_maddy Source code
compare_matrix_control Source code
compare_models Man page Source code
compute_partitions Source code
connect_tips Source code
convert_counts_matrix Man page Source code
copy_reduce_dim_aux Source code
count_nn_missing_self_index Source code
counts_row_order Man page
counts_row_order,cell_data_set-method Man page
detect_genes Man page Source code
edit_query_cell_labels Source code
enrichment_matrix Source code
estimate_sf_bpcells Source code
estimate_sf_dense Source code
estimate_sf_sparse Source code
estimate_size_factors Man page Source code
evaluate_fits Man page
exprs Man page
exprs,cell_data_set-method Man page
extract_coefficient_helper Source code
extract_general_graph_ordering Source code
extract_model_status_helper Source code
fData Man page
fData,cell_data_set-method Man page
fData<- Man page
fData<-,cell_data_set-method Man page
file_permission_o2rws Source code
file_permission_os2rwx Source code
findNearestPointOnMST Source code
find_gene_modules Man page Source code
find_nearest_vertex Source code
fit_model_helper Source code
fit_models Man page Source code
fix_missing_cell_labels Man page Source code
generate_centers Man page Source code
generate_garnett_marker_file Man page Source code
get_call_stack_as_string Source code
get_cds_nn_control Source code
get_cds_nn_index Source code
get_cds_nn_search Source code
get_citations Man page Source code
get_counts_identity Source code
get_genome_in_matrix_path Man page Source code
get_global_variable Source code
get_matrix_class Source code
get_matrix_info Source code
get_nn_cell_label Source code
get_nn_means Source code
get_reduce_dim_matrix_identity Source code
get_reduce_dim_model_identity Source code
get_time_stamp Source code
get_unique_id Source code
graph_test Man page Source code
has_nn_index Source code
identity_as_string Source code
identity_table Man page Source code
initialize_counts_metadata Source code
initialize_reduce_dim_metadata Source code
initialize_reduce_dim_model_identity Source code
is_matrix Source code
is_matrix_market_file Source code
is_sparse_matrix Source code
jaccard_coeff Source code
leaf_nodes Source code
learn_graph Man page Source code
leiden_clustering Source code
load_a549 Man page Source code
load_annotations_data Source code
load_annoy_index Source code
load_bpcells_matrix_dir Source code
load_cellranger_data Man page Source code
load_hnsw_index Source code
load_mm_data Man page Source code
load_monocle_objects Man page Source code
load_monocle_rds Source code
load_mtx_data Man page Source code
load_transform_models Man page Source code
load_umap_annoy_index Source code
load_umap_nn_indexes Source code
load_worm_embryo Man page Source code
load_worm_l2 Man page Source code
louvain_clustering Source code
make_cds_nn_index Man page Source code
make_nn_index Man page Source code
make_tar_of_dir Source code
makeprobs Source code
makeprobsvec Source code
matrix_multiply_multicore Source code
mc_es_apply Man page Source code
model_predictions Man page
monocle_theme_opts Source code
multi_component_RGE Source code
my.dMcast Source code
new_annoy_index Source code
new_cell_data_set Man page Source code
normalize_expr_data Source code
normalized_counts Man page Source code
object_name_to_string Source code
order_cells Man page Source code
pData Man page
pData,cell_data_set-method Man page
pData<- Man page
pData<-,cell_data_set-method Man page
partitions Man page
partitions,cell_data_set-method Man page
plot_cells Man page
plot_cells_3d Man page Source code
plot_cells_per_sample_and_perturbation Man page
plot_genes_by_group Man page
plot_genes_hybrid Man page
plot_genes_in_pseudotime Man page
plot_genes_violin Man page
plot_mito_umi_per_cell Man page
plot_pc_variance_explained Man page
plot_percent_cells_positive Man page
plot_umi_per_cell Man page
plot_umi_per_cell_and_perturbation Man page
pnorm_over_mat Source code
preprocess_cds Man page Source code
preprocess_transform Man page Source code
principal_graph Man page
principal_graph,cell_data_set-method Man page
principal_graph<- Man page
principal_graph<-,cell_data_set-method Man page
principal_graph_aux Man page
principal_graph_aux,cell_data_set-method Man page
principal_graph_aux<- Man page
principal_graph_aux<-,cell_data_set-method Man page
projPointOnLine Source code
project2MST Source code
project_point_to_line_segment Source code
prune_tree Source code
pseudotime Man page
pseudotime,cell_data_set-method Man page
push_matrix_path Source code
reduce_dimension Man page Source code
reduce_dimension_transform Man page Source code
repmat Man page Source code
report_checksum_difference Source code
report_files_saved Source code
report_nn_control Source code
report_path_status Source code
rm_bpcells_dir Source code
root_nodes Source code
save_annoy_index Source code
save_hnsw_index Source code
save_monocle_objects Man page Source code
save_transform_models Man page Source code
save_umap_annoy_index Source code
save_umap_nn_indexes Source code
search_cds_nn_index Man page Source code
search_nn_annoy_index Source code
search_nn_index Man page Source code
search_nn_matrix Man page Source code
select_annoy_search_k Source code
select_matrix_parameter_value Source code
select_nn_parameter_value Source code
select_trajectory_roots Source code
set_archive_control Source code
set_cds_nn_index Man page Source code
set_cds_nn_search Source code
set_cds_row_order_matrix Man page Source code
set_counts_identity Source code
set_global_variable Source code
set_matrix_citation Source code
set_matrix_class Source code
set_matrix_control Man page Source code
set_matrix_control_combine_cds Source code
set_matrix_control_default Source code
set_matrix_control_pca Source code
set_model_identity_path Source code
set_nn_control Man page Source code
set_reduce_dim_matrix_identity Source code
set_reduce_dim_model_identity Source code
shannon.entropy Source code
show_matrix_control Source code
show_matrix_info Source code
size_factors Man page Source code
size_factors<- Man page
smart_es_apply Source code
soft_assignment Man page Source code
sparse_apply Source code
sparse_apply_transform Source code
sparse_prcomp_irlba Man page Source code
specificity_matrix Source code
stop_no_noise Source code
svd_rebuild_matrix Source code
swap_nn_row_index_point Source code
tasks_per_block Source code
test_annoy_index Source code
test_hdf5_assays Source code
test_hnsw_index Source code
test_marker_for_cell_group Source code
tfidf Source code
tick Source code
tock Source code
top_markers Man page Source code
transfer_cell_labels Man page Source code
update_annoy_index Source code
update_hnsw_index Source code
which_mode Source code
cole-trapnell-lab/monocle3 documentation built on June 11, 2025, 11:22 p.m.

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