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This is the API documentation for the harmonizome library.
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## Core API

Public Harmonizome client objects


Harmonizome()

Entity


## Harmonizome Methods

Methods for the Harmonizome class


get(entity: str, name: Optional[str] = None, start_at: Optional[int] = None) -> dict[str, typing.Any]

Returns a single entity or a list, depending on if a name is
provided. If no name is provided and start_at is specified, returns a
list starting at that cursor position.

next(response: dict[str, typing.Any]) -> dict[str, typing.Any]

Returns the next set of entities based on a previous API response.

download(datasets: Optional[list[str]] = None, what: Optional[list[str]] = None) -> collections.abc.Iterator[str]

For each dataset, creates a directory and downloads files into it.

download_df(datasets: Optional[list[str]] = None, what: Optional[list[str]] = None, sparse: bool = False, **kwargs: Any) -> collections.abc.Iterator[pandas.DataFrame]

get_gene_functional_annotations(gene_symbol: str, datasets: Optional[list[str]] = None) -> dict[str, typing.Any]

Get functional annotations for a gene using the Harmonizome API.

This method uses the API directly without downloading any files.
It leverages the showAssociations=true parameter to get functional
associations for a gene.

Args:
    gene_symbol: Gene symbol (e.g., 'BRCA1', 'STAT3')
    datasets: List of dataset names to search. If None, searches all datasets.

Returns:
    Dictionary formatted like Harmonizome web interface with:
    - gene_info: Basic gene information
    - functional_associations: List of datasets with associations

get_gene_with_associations(gene_symbol: str) -> dict[str, typing.Any]

Get gene information with associations using the API.

This uses the showAssociations=true parameter to get functional
associations directly from the API without downloading files.

Args:
    gene_symbol: Gene symbol

Returns:
    Dictionary with gene info and associations

download_gene_functional_annotations(gene_symbol: str, datasets: Optional[list[str]] = None) -> dict[str, typing.Any]

Download and get all functional annotations for a gene across specified datasets.

This method downloads the necessary data files and extracts associations
for the specified gene from the gene-attribute matrices.

Args:
    gene_symbol: Gene symbol (e.g., 'BRCA1', 'STAT3')
    datasets: List of dataset names to search. If None, searches all datasets.

Returns:
    Dictionary with dataset names as keys and annotation data as values.

get_gene_associations_summary(gene_symbol: str, datasets: Optional[list[str]] = None, use_download: bool = False) -> dict[str, typing.Any]

Get a summary of all functional associations for a gene.

Args:
    gene_symbol: Gene symbol
    datasets: List of dataset names to search. If None, searches all datasets.
    use_download: If True, downloads files to get associations. If False, uses API.

Returns:
    Dictionary with summary statistics and dataset breakdown

get_gene_functional_associations_formatted(gene_symbol: str, datasets: Optional[list[str]] = None, use_download: bool = False) -> dict[str, typing.Any]

Get functional associations for a gene in Harmonizome web interface format.

This method returns data structured exactly like the Harmonizome web interface,
with datasets, summaries, and categorized associations with scores.

Args:
    gene_symbol: Gene symbol (e.g., 'STAT3', 'BRCA1')
    datasets: List of dataset names to search. If None, searches all datasets.
    use_download: If True, downloads files to get associations. If False, uses API.

Returns:
    Dictionary formatted like Harmonizome web interface with:
    - gene_info: Basic gene information
    - functional_associations: List of datasets with associations

get_gene_data(gene_symbol: str, use_cache: bool = False) -> harmonizome.harmonizome.GeneData