Python API reference

This reference lists the Python functions, classes, methods and attributes in RustScenic, including their source signatures, parameter defaults and available docstrings. Start with the API map to choose a stage or the quickstart to prepare a workflow.

Module Contents
rustscenic.grn Gene-network inference, correlation, regulon construction and TF-list loading.
rustscenic.aucell Per-cell regulon activity scores.
rustscenic.cistarget Motif enrichment, annotation-based pruning and ranking-file loading.
rustscenic.topics Topic fitting, coherence, assignment summaries and result containers.
rustscenic.preproc Fragment matrices, peak calling and the qc namespace of quality-control functions.
rustscenic.enhancer Peak-to-gene links from RNA, ATAC and gene coordinates.
rustscenic.eregulon eRegulon objects, dataframe assembly and conversion helpers.
rustscenic.specificity Regulon specificity scores and candidate enhancers per topic.
rustscenic.pipeline The staged orchestrator and its result manifest.
rustscenic.data Bundled TF lists and cached motif-ranking and gene-coordinate resources.
rustscenic.backend Installed-backend checks and the required Rust symbol groups.
rustscenic.cli Python entry points behind the rustscenic command. Handlers receive the argparse.Namespace assembled by main; use the command line for normal interactive use.
rustscenic.quickstart Entry point for python -m rustscenic.quickstart.

Reading the reference

Each module page includes its own public definitions and first-party helpers reexported under public names. Private names beginning with _ and imported third-party APIs are excluded. The explicitly implemented ERegulon.__len__ protocol is included. Reexports describe the same underlying implementation; they do not introduce additional analysis stages.

Signatures include all parameters, their available type annotations and defaults. Dataclass constructor signatures include their fields; list() and dict() represent a fresh value from a default factory. The array and dictionary result subclasses inherit their base constructors.

The reference is collected statically from this source tree. It does not import RustScenic or load its compiled extension during the documentation build. Other documentation projects can use the generated Sphinx-compatible object inventory to cross-reference these APIs.

Package exports

Analysis modules are documented on the pages above. The package also reexports backend_capabilities and the installed extension's __version__ value.

rustscenic

rustscenic: fast SCENIC+ stage replacements.

__version__ module-attribute 

__version__: str

backend_capabilities 

backend_capabilities() -> dict[str, Any]

Record Rust extension symbols required by the benchmarked pipeline.

Returns:

Type Description
dict[str, Any]

ok, extension_error, required_symbols and missing_symbols describing the installed extension.