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API Reference

High-Level Functions

Function Description
secact_activity_inference() Bulk RNA-seq inference
secact_activity_inference_scrnaseq() scRNA-seq inference
secact_activity_inference_st() Spatial transcriptomics inference
load_signature(name='secact') Load built-in signature matrix

Core Functions

Function Description
ridge() Single-call ridge regression with permutation testing
ridge_batch() Batch processing for large datasets (dense or sparse)
ridge_batch_streaming() Two-pass streaming inference for >5M-cell H5AD files
H5ADChunkReader Memory-efficient chunk reader for H5AD files via h5py
estimate_batch_size() Estimate optimal batch size for available memory
estimate_memory() Estimate memory requirements

Key Parameters

Parameter Default Description
sig_matrix "secact" Signature: "secact", "cytosig", or DataFrame
lambda_ 5e5 Ridge regularization parameter
n_rand 1000 Number of permutations
seed 0 Random seed for reproducibility
rng_method None RNG backend: 'srand' (match R, default), 'gsl' (cross-platform), 'numpy' (fast). None defaults to srand.
is_group_sig True Group similar signatures by correlation before regression
backend 'auto' 'auto', 'numpy', or 'cupy'
use_cache False Cache permutation tables to disk
sparse_mode False Keep sparse Y in sparse format (avoids densification)
col_center True Subtract column means during sparse in-flight normalization
col_scale True Divide by column stds during sparse in-flight normalization

ST-Specific Parameters

Parameter Default Description
cell_type_col None Column in AnnData.obs for cell type
is_spot_level True If False, aggregate by cell type
scale_factor 1e5 Normalization scale factor

Batch Processing Parameters

Parameter Default Description
batch_size None Samples per batch (None = all at once)
output_path None Stream results to H5AD file (requires batch_size)
output_compression "gzip" Compression: "gzip", "lzf", or None

Streaming H5AD Parameters

These parameters are available on secact_activity_inference_scrnaseq() and secact_activity_inference_st() for processing >5M-cell datasets that exceed available RAM.

Parameter Default Description
streaming False Enable two-pass chunk reading from H5AD (requires file path input, not AnnData)
streaming_chunk_size 50_000 Number of cells per H5AD read chunk

For low-level ridge() / ridge_batch() usage and sparse column normalization details, see Advanced API.