Jaspar Tools¶
Configuration File: jaspar_tools.json
Tool Type: Local
Tools Count: 8
This page contains all tools defined in the jaspar_tools.json configuration file.
Available Tools¶
JASPAR_get_transcription_factors (Type: JASPARRESTTool)¶
List transcription factor binding site matrices (PFMs/PWMs metadata) from JASPAR. Use this to bro…
JASPAR_get_transcription_factors tool specification
Tool Information:
Name:
JASPAR_get_transcription_factorsType:
JASPARRESTToolDescription: List transcription factor binding site matrices (PFMs/PWMs metadata) from JASPAR. Use this to browse matrices and discover matrix_id values for downstream tools like jaspar_get_matrix.
Parameters:
collection(string) (optional) JASPAR collection (e.g., CORE).page(integer) (optional) Page number (1-based).page_size(integer) (optional) Results per page (JASPAR page_size).
Example Usage:
query = {
"name": "JASPAR_get_transcription_factors",
"arguments": {
}
}
result = tu.run(query)
jaspar_get_matrix (Type: JASPARRESTTool)¶
Get full details for a single JASPAR matrix by matrix_id (e.g., MA0002.2). Returns metadata plu…
jaspar_get_matrix tool specification
Tool Information:
Name:
jaspar_get_matrixType:
JASPARRESTToolDescription: Get full details for a single JASPAR matrix by matrix_id (e.g., MA0002.2). Returns metadata plus PFM/PWM. For reproducible analyses, use jaspar_get_matrix_versions with the corresponding base_id (e.g., MA0002) to see all versions and choose/cite the exact version you used.
Parameters:
matrix_id(string) (required) JASPAR matrix ID (e.g., ‘MA0002.2’). You can discover IDs with JASPAR_get_transcription_factors.
Example Usage:
query = {
"name": "jaspar_get_matrix",
"arguments": {
"matrix_id": "example_value"
}
}
result = tu.run(query)
jaspar_get_matrix_versions (Type: JASPARRESTTool)¶
List all versions available for a JASPAR matrix base ID (e.g., base_id MA0002). This is useful fo…
jaspar_get_matrix_versions tool specification
Tool Information:
Name:
jaspar_get_matrix_versionsType:
JASPARRESTToolDescription: List all versions available for a JASPAR matrix base ID (e.g., base_id MA0002). This is useful for reproducibility (choose a specific matrix version like MA0002.2) and for tracking updates across releases.
Parameters:
base_id(string) (required) JASPAR base matrix ID without version (e.g., ‘MA0002’). You can get base_id from jaspar_get_matrix.page(integer) (optional) Page number (1-based).page_size(integer) (optional) Results per page.
Example Usage:
query = {
"name": "jaspar_get_matrix_versions",
"arguments": {
"base_id": "example_value"
}
}
result = tu.run(query)
jaspar_list_collections (Type: JASPARRESTTool)¶
List JASPAR collections (e.g., CORE, CNE). Useful for filtering matrices by collection.
jaspar_list_collections tool specification
Tool Information:
Name:
jaspar_list_collectionsType:
JASPARRESTToolDescription: List JASPAR collections (e.g., CORE, CNE). Useful for filtering matrices by collection.
Parameters:
No parameters required.
Example Usage:
query = {
"name": "jaspar_list_collections",
"arguments": {
}
}
result = tu.run(query)
jaspar_list_releases (Type: JASPARRESTTool)¶
List available JASPAR releases (database version history). Useful for research reproducibility: r…
jaspar_list_releases tool specification
Tool Information:
Name:
jaspar_list_releasesType:
JASPARRESTToolDescription: List available JASPAR releases (database version history). Useful for research reproducibility: record which JASPAR release you used when selecting motifs, or check what releases exist before comparing results across versions.
Parameters:
page(integer) (optional) Page number (1-based).page_size(integer) (optional) Results per page.
Example Usage:
query = {
"name": "jaspar_list_releases",
"arguments": {
}
}
result = tu.run(query)
jaspar_list_species (Type: JASPARRESTTool)¶
List species available in JASPAR (taxonomy IDs + names). Useful for filtering matrices by species.
jaspar_list_species tool specification
Tool Information:
Name:
jaspar_list_speciesType:
JASPARRESTToolDescription: List species available in JASPAR (taxonomy IDs + names). Useful for filtering matrices by species.
Parameters:
page(integer) (optional) Page number (1-based).page_size(integer) (optional) Results per page.
Example Usage:
query = {
"name": "jaspar_list_species",
"arguments": {
}
}
result = tu.run(query)
jaspar_list_taxa (Type: JASPARRESTTool)¶
List available taxonomic groups (taxa) in JASPAR (e.g., vertebrates, plants). Useful for filterin…
jaspar_list_taxa tool specification
Tool Information:
Name:
jaspar_list_taxaType:
JASPARRESTToolDescription: List available taxonomic groups (taxa) in JASPAR (e.g., vertebrates, plants). Useful for filtering matrices by tax_group.
Parameters:
No parameters required.
Example Usage:
query = {
"name": "jaspar_list_taxa",
"arguments": {
}
}
result = tu.run(query)
jaspar_search_matrices (Type: JASPARRESTTool)¶
Search/filter JASPAR matrices using common query parameters. Typical filters include search (fr…
jaspar_search_matrices tool specification
Tool Information:
Name:
jaspar_search_matricesType:
JASPARRESTToolDescription: Search/filter JASPAR matrices using common query parameters. Typical filters include search (free text), name, collection, tax_group, species, and paging via page/page_size.
Parameters:
search(string) (optional) Free-text search across matrices (e.g., ‘CTCF’).name(string) (optional) Filter by TF name (e.g., ‘CTCF’).collection(string) (optional) Filter by collection (e.g., ‘CORE’).tax_group(string) (optional) Filter by taxonomic group (e.g., ‘vertebrates’).species(string) (optional) Filter by NCBI taxonomy ID (e.g., ‘9606’ for human).page(integer) (optional) Page number (1-based).page_size(integer) (optional) Results per page.
Example Usage:
query = {
"name": "jaspar_search_matrices",
"arguments": {
}
}
result = tu.run(query)