omicverse.single.cNMF

omicverse.single.cNMF(adata, components, n_iter=100, densify=False, tpm_fn=None, seed=None, beta_loss='frobenius', num_highvar_genes=2000, genes_file=None, alpha_usage=0.0, alpha_spectra=0.0, init='random', output_dir=None, name=None, use_gpu=True, gpu_id=0)[source]

Consensus NMF workflow wrapper for robust gene-program discovery.

Parameters:

  • adata (AnnData) – Input single-cell expression AnnData.

  • components (array-like) – Candidate rank values (number of programs/topics) to evaluate.

  • n_iter (int, default=100) – Number of NMF restarts per rank.

  • output_dir (str, optional) – Directory used to store temporary and result files.

  • name (str, optional) – Analysis name prefix for output artifacts.

  • use_gpu (bool, default=True) – Whether to use GPU-accelerated factorization when available.

  • gpu_id (int, default=0) – CUDA device index.