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_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_enrichment(): UI - Module Enrichment

ui_module_metadata_heatmap(): UI - Gene Module Heatmap

ui_module_umap(): UI - Gene Module UMAP

ui_pseudotime_select_cells(): UI - Pseudotime

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_enrichment(): Server - Module Enrichment

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

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

Monocle3 Utilities

custom_learn_graph(): Learn the graph of the Monocle object

custom_pseudotime_ordering(): Order the cells by pseudotime

diet_monocle_object(): Diet Monocle object

get_pseudotime_recommendation(): Recommend a pseudotime ordering

subset_monocle_by_trajectory(): Subset the Monocle object by a trajectory

update_monocle_partition(): Update the partition of the Monocle object

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