API for cole-trapnell-lab/monocle3
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Global functions
`size_factors<-` Source code
add_citation Source code
aggregate_gene_expression Man page Source code
align_cds Man page Source code
branch_nodes Source code
cal_ncenter Source code
calc_principal_graph Man page Source code
calculateLW Man page Source code
cell_data_set Man page
cell_data_set-class Man page
cell_data_set-methods Man page
choose_cells Man page Source code
choose_graph_segments Man page 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_slots Man page Source code
cluster_cells Man page Source code
clusters Man page
clusters,cell_data_set-method Man page
coefficient_table Man page Source code
combine_cds Man page Source code
compare_models Man page Source code
compute_partitions Source code
connect_tips Source code
detect_genes Man page Source code
enrichment_matrix 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
findNearestPointOnMST Source code
find_gene_modules Man page Source code
find_nearest_vertex Man page Source code
fit_model_helper Man page Source code
fit_models Man page Source code
generate_centers Man page Source code
generate_garnett_marker_file Man page Source code
get_citations Man page Source code
get_genome_in_matrix_path Man page Source code
graph_test Man page 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_cellranger_data Man page Source code
load_mm_data Man page Source code
load_mtx_data Man page Source code
load_worm_embryo Man page Source code
louvain_clustering Source code
makeprobs Source code
makeprobsvec Source code
mc_es_apply Man page Source code
model_predictions Man page
monocle_theme_opts Source code
multi_component_RGE Source code
my.aggregate.Matrix Man page
new_cell_data_set Man page Source code
normalize_expr_data Source code
normalized_counts Man page 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_genes_by_group Man page
plot_genes_in_pseudotime Man page
plot_genes_violin Man page
plot_pc_variance_explained Man page
plot_percent_cells_positive Man page
pnorm_over_mat Source code
preprocess_cds 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
reduce_dimension Man page Source code
repmat Man page Source code
root_nodes Source code
select_trajectory_roots Source code
shannon.entropy 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_prcomp_irlba Man page Source code
specificity_matrix Source code
test_marker_for_cell_group Source code
tfidf Source code
top_markers Man page Source code
cole-trapnell-lab/monocle3 documentation built on April 8, 2021, 5:54 a.m.