Package index • unitcm

Infrastructure

HTTP client, authentication, and pagination helpers.

set_base_url(): Set the UniTCM API base URL
get_base_url(): Get the UniTCM API base URL
set_unitcm_token(): Set a UniTCM API token
get_unitcm_token(): Get the UniTCM API token
clear_unitcm_token(): Clear the UniTCM API token
set_api_key(): Set a UniTCM API Key
get_api_key(): Get the UniTCM API Key
clear_api_key(): Clear the UniTCM API Key
flatten_response(): Flatten a nested API response to a tibble
unitcm_cache_clear(): Clear unitcm cache

TCMomics Database

Browse and search multi-omics datasets.

search_datasets(): Search TCMomics datasets
get_dataset(): Get a single dataset by submission ID
get_similar_datasets(): Get similar datasets
fetch_dataset_facets(): Get dataset facets
fetch_dataset_stats(): Get TCMomics database statistics
export_datasets(): Export datasets to CSV

Home & Statistics

Platform-level statistics and latest submissions.

fetch_home_stats(): Get homepage statistics
fetch_latest_submissions(): Get latest submissions
fetch_tcm_classification_stats(): Get TCM classification statistics
fetch_omics_type_stats(): Get omics type statistics

Herb Explorer

Query herbs, their properties, and associated compounds.

search_herbs(): Search herbs in the Herb Explorer
get_herb(): Get a single herb by ID
fetch_herb_facets(): Get herb filter facets
get_herb_compounds(): Get compounds for a herb
export_herbs(): Export herbs to CSV
export_herb_compounds(): Export herb compounds to CSV

Ingredient Explorer

Query compounds, ADMET predictions, and target predictions.

search_compounds(): Search compounds in the Ingredient Explorer
get_compound(): Get a single compound by ID
get_compound_admet(): Get ADMET predictions for a compound
get_compound_targets(): Get predicted targets for a compound
get_compound_herbs(): Get herbs containing a compound
fetch_compound_facets(): Get compound facets and statistics
export_compounds(): Export compounds to CSV
export_compound_module(): Export compound data by module

Disease-Formula Atlas

Query disease-formula associations and ICD-11 classification.

search_formulas(): Search formulas in the Disease-Formula Atlas
get_formula(): Get a single formula by order ID
get_formula_doses(): Get herb doses for a formula
fetch_disease_tree(): Get the ICD-11 disease classification tree
list_book_sources(): List book sources
list_origin_sources(): List origin sources
list_dosage_forms(): List dosage forms

TCM Ontology

Navigate and search the TCM ontology hierarchy.

search_ontology(): Search the TCM Ontology
get_ontology_entity(): Get a TCM ontology entity
get_ontology_children(): Get children of an ontology entity
get_ontology_descendants(): Get all descendants of an ontology entity
get_ontology_ancestors(): Get ancestors of an ontology entity
fetch_ontology_tree(): Fetch the TCM ontology tree
fetch_ontology_stats(): Fetch ontology statistics
list_ontology_categories(): List top-level ontology categories
get_ontology_by_level(): Get ontology entities by level
search_ontology_mapping(): Search ontology external mapping
export_ontology(): Export the TCM ontology

MIDAS Gene-Disease

Multi-source gene-disease association analysis.

query_gene_diseases(): Query gene-to-disease associations (MIDAS)
query_disease_genes(): Query disease-to-gene associations (MIDAS)
convert_gene_ids(): Convert gene identifiers (MIDAS)
query_disease_enrichment(): Disease enrichment analysis (MIDAS)
query_source_comparison(): Compare gene-disease sources (MIDAS)
query_disease_intersection(): Find disease intersection (MIDAS)
autocomplete_disease(): Autocomplete disease names (MIDAS)
fetch_midas_sources(): Get MIDAS data sources
fetch_midas_stats(): Get MIDAS statistics

TCM Terms & Mechanisms

Search TCM terms and their modern mechanisms.

search_terms(): Search TCM bilingual corpus terms
get_term(): Get a single term by ID
list_term_sources(): List term sources
list_term_categories(): List term categories
search_mechanisms(): Search terms molecular mechanisms
get_mechanism(): Get a single mechanism term by ID
fetch_mechanism_filters(): Get mechanism filter options

Transcriptome Hub

Query TCM transcriptomics datasets and analysis results.

search_transcriptomes(): Search transcriptome datasets
get_transcriptome(): Get a single transcriptome dataset
fetch_transcriptome_filters(): Get transcriptome filter options
fetch_transcriptome_stats(): Get Transcriptome Hub statistics
get_analysis_modules(): List available analysis modules for a dataset
get_analysis_data(): Get analysis data for a transcriptome dataset

NetVis

Network pharmacology graph queries.

fetch_netvis_stats(): Get NetVis network statistics
search_netvis(): Search NetVis nodes
get_neighbors(): Get neighbors of a node
get_subgraph(): Get subgraph for a set of nodes
find_path(): Find shortest path between two nodes
get_node_detail(): Get node detail
get_node_metrics(): Get node metrics
detect_communities(): Detect communities in a graph

Network Helpers

Build and convert network objects locally.

build_hct_network(): Build an Herb-Compound-Target network
build_formula_herb_network(): Build a Formula-Herb network
as_igraph(): Convert a NetVis graph response to igraph
as_tidygraph(): Convert a NetVis graph response to tidygraph

Visualization

Quick plotting helpers.

plot_network(): Plot a network graph
plot_enrichment(): Plot enrichment results
plot_compound_radar(): Plot compound physicochemical radar chart

PPI & Enrichment

Protein-protein interaction networks and GO/KEGG enrichment via STRING and Enrichr APIs.

query_string_ppi(): Query the STRING database for protein-protein interactions
build_ppi_network(): Build a PPI network as an igraph object
identify_hub_genes(): Identify hub genes by degree centrality
louvain_cluster(): Detect communities in a PPI network using the Louvain algorithm
enrichr_enrichment(): Perform GO and KEGG pathway enrichment via the Enrichr API

Network Separation

Network-based separation analysis (Menche et al. 2015) to quantify drug-target-to-disease-module proximity.

set_distance(): Compute closest distance between two gene sets in a network
self_distance(): Compute mean internal distance of a gene set
network_separation(): Compute the network separation score S_AB
per_node_distance(): Compute per-node closest distance to another gene set
find_elbow(): Find the elbow (knee) point in a curve
find_saturation_point(): Find the saturation point in a curve
network_separation_sweep(): Sweep network separation across top-N gene selection
network_separation_analysis(): Network separation analysis

Target2NP

Reverse target-to-natural-product search across DrugCLIP and SEA.

search_target2np(): Search Target2NP compound-target interactions
search_target2np_drugclip(): Search DrugCLIP predicted compound-target interactions
search_target2np_sea(): Search SEA (ChEMBL similarity) predicted compound-target interactions
get_target2np(): Get a single Target2NP interaction record
batch_target2np(): Batch query Target2NP by identifier list
aggregated_target2np(): Aggregated Target2NP view across data sources
target2np_multi_source_summary(): Multi-source summary for a Target2NP query
fetch_target2np_filters(): Fetch Target2NP filter options
fetch_target2np_stats(): Fetch Target2NP database statistics