Package index • Starlng

Shiny Write Utilities

starlng_write_app_clustassess(): Create Starlng Shiny app from a ClustAssess object

starlng_write_app_clustassess_app(): Create Starlng Shiny app from a ClustAssess object

starlng_write_app_default(): Create Starlng Shiny app from a normalized gene expression matrix

starlng_write_app_monocle(): Create Starlng Shiny app from Monocle object

Shiny App Components

ui_functional_assessment(): UI - Functional Assessment

ui_gene_clustering(): UI - Gene clustering

ui_gene_info_table(): UI - Gene Info Table

ui_gene_umap(): UI - Gene UMAP

ui_global_setttings(): UI - Global Settings

ui_metadata_umap(): UI - Metadata UMAP

ui_module_metadata_heatmap(): UI - Gene Module Heatmap

ui_module_umap(): UI - Gene Module UMAP

ui_pseudotime_select_cells(): UI - Pseudotime

server_functional_assessment(): Server - Functional Assessment

server_gene_clustering(): Server - Gene clustering

server_gene_info_table(): Server - Gene Info Table

server_gene_umap(): Server - Gene UMAP

server_metadata_umap(): Server - Metadata UMAP

server_module_metadata_heatmap(): Server - Gene Module Heatmap

server_module_umap(): Server - Gene Module UMAP

server_pseudotime_select_cells(): Server - Pseudotime

prepare_session(): Server - Prepare Session

update_gears_width(): Server - Gear Width

update_tabs(): Server - Tabs update

Gene/Cell Utilities

filter_central_cells_from_group(): Find central points of a group

remove_outlier_cells(): Remove outlier cells from a group

select_cells_by_gene_expr(): Select cells by gene expression

select_cells_by_metadata(): Select cells by metadata

calculate_umap_average_distance(): Calculate Average UMAP Distance

voting_scheme(): Gene Expression voting scheme

read_gene_from_dense_h5(): Read expression matrix from a dense HDF5 file

sort_genes_by_metadata(): Sort genes by metadata information

write_gene_matrix_dense_h5(): Write expression matrix to a dense HDF5 file

write_gene_matrix_sparse_h5(): Write expression matrix to a sparse HDF5 file

plot_umap(): Plot UMAP with Discrete or Continuous Coloring

Monocle3 Utilities

diet_monocle_object(): Diet Monocle object

subset_monocle_by_trajectory(): Subset the Monocle object by a trajectory

update_monocle_partition(): Update the partition of the Monocle object

Pseudotime Utilities

custom_learn_graph(): Learn the graph of the Monocle object

get_trajectory_object(): Build a Trajectory Helper Object

plot_trajectory_graph(): Plot a Trajectory Graph

custom_pseudotime_ordering(): Order the cells by pseudotime

get_pseudotime_recommendation(): Recommend a pseudotime ordering

order_metadata_groups_by_pseudotime(): Order Metadata Groups by Pseudotime

Stability Utilities

clustering_pipeline(): Community detection pipeline

community_detection_master(): Community detection wrapper

get_clusters_consistency(): Get the by-cluster consistency of configurations

get_feature_loading(): Get feature loading from an expression matrix

group_by_clusters_general(): Group the partitions by the number of clusters

parallel_nn2_idx(): Parallel NN indexing

pca_reduction(): Get PCA reduction from an expression matrix

select_best_configuration(): Select the most stable configurations of parameters

Module Processing

build_module_masks(): Build Module Masks

compute_module_pairwise_tables(): Compute Module Pairwise Tables

detect_outlier(): Detect Module Outliers

get_closest_node_to_module(): Find Closest Trajectory Node to Module

get_filtered_gene_adjacency(): Filter Gene Adjacency by Module Structure

get_module_centroid(): Compute Module Centroid in Embedding Space

get_module_stats(): Compute Module Statistics

get_module_transitions(): Build Module Transition Adjacency

plot_module_transitions(): Plot Module Transition Graph

summarise_module_stats(): Summarize Module Statistics

get_per_module_weight(): Compute Per-Module Gene Weights

get_gene_overlap_stat(): Compute Gene Hub Statistics

plot_umap_gene_modules(): Plot UMAP for Multiple Gene Modules

plot_module_pseudobulk_expression(): Plot Module Pseudobulk Expression

generate_cell_heatmap(): Generate Cell Heatmap

plot_gene_hub_umap(): Plot Gene UMAP with Hub Highlighting

plot_module_trends_over_pseudotime(): Plot Module Trends over Pseudotime

Enrichment Analysis

filter_enrichment_results(): Filter Enrichment Results

plot_enrichment_top_terms(): Plot Top Enriched Terms

TF Analysis

get_transcription_factors(): Get Enriched Transcription Factors

get_tf_stats(): Summarize Transcription Factor Statistics

add_tf_hub_stats(): Add Hub-Gene Counts to TF Statistics

get_tf_gene_network(): Build TF-Gene Network Graph

plot_module_tfs_ggraph(): Plot TF-Gene Network with ggraph

plot_module_tfs_bubbleplot(): Plot TF Bubble Plot