signaturescoring package

Subpackages

• signaturescoring.scoring_methods package
  • Submodules
  • signaturescoring.scoring_methods.adjusted_neighborhood_scoring module
    • score_genes()
  • signaturescoring.scoring_methods.compute_signature_score module
    • compute_signature_score()
  • signaturescoring.scoring_methods.corrected_scanpy_scoring module
    • score_genes()
  • signaturescoring.scoring_methods.gene_signature_scoring module
    • score_signature()
  • signaturescoring.scoring_methods.gmm_postprocessing module
    • GMMPostprocessor
      • GMMPostprocessor.assign_clusters_to_signatures()
      • GMMPostprocessor.fit_and_predict()
    • check_score_names()
  • signaturescoring.scoring_methods.jasmine_scoring module
    • compute_avg_ranks_sig_subset()
    • compute_avg_ranks_signature()
    • likelihood_calculation()
    • or_calculation()
    • preparation()
    • rank_calculation()
    • score_genes()
  • signaturescoring.scoring_methods.neighborhood_scoring module
    • score_genes()
  • signaturescoring.scoring_methods.seurat_ag_scoring module
    • score_genes()
  • signaturescoring.scoring_methods.seurat_lvg_scoring module
    • score_genes()
  • signaturescoring.scoring_methods.seurat_scoring module
    • score_genes()
  • signaturescoring.scoring_methods.ucell_scoring module
    • compute_ranks_and_ustat()
    • score_genes()
    • u_stat()
  • Module contents
• signaturescoring.utils package
  • Submodules
  • signaturescoring.utils.metrics module
    • get_AUC_and_F1_performance()
    • get_test_statistics()
  • signaturescoring.utils.utils module
    • check_signature_genes()
    • checks_ctrl_size()
    • commonPrefix()
    • commonPrefixUtil()
    • get_bins_wrt_avg_gene_expression()
    • get_data_for_gene_pool()
    • get_gene_list_real_data()
    • get_least_variable_genes_per_bin_v1()
    • get_least_variable_genes_per_bin_v2()
    • get_mean_and_variance_gene_expression()
    • nanmean()
    • nextnonexistent()
  • Module contents

Module contents

signaturescoring.score_signature(adata: AnnData, gene_list: List[str], method: str = 'adjusted_neighborhood_scoring', **kwarg) → AnnData | None

Wrapper method to call one of the available gene expression signature scoring methods (ANS, Seurat, Seurat_AG, Seurat_LVG, Scanpy, Jasmine, UCell).

Parameters:

• adata – AnnData object containing the gene expression data.

• gene_list – A list of genes,i.e., gene expression signature, for which the cells are scored for.

• method – Scoring method to use. One of [‘adjusted_neighborhood_scoring’, ‘seurat_scoring’, ‘seurat_ag_scoring’, ‘seurat_lvg_scoring’, ‘scanpy_scoring’, ‘jasmine_scoring’, ‘ucell_scoring’, ‘neighborhood_scoring’, ‘corrected_scanpy_scoring’]

• **kwarg – Other keyword arguments specific for the scoring method. See below names of individual scoring methods and their available keyword arguments.

Returns:

If copy=True, the method returns a copy of the original data with stored ANS scores in .obs, otherwise None is returned.

Notes

ANS: Adujsted neighborhood signature scoring method.

(see signaturescoring.scoring_methods.adjusted_neighborhood_scoring.score_genes) 10.1126/science.aad0501, (see signaturescoring.scoring_methods.seurat_scoring.score_genes)

Seurat_AG, Seurat_LVG: Modifications of above method. First selecting all genes in an expression bin as control genes. Latter selecting the least variable genes of an expression bin as control genes.

(see signaturescoring.scoring_methods.seurat_[ag/lvg]_scoring.score_genes)

Scanpy: Scoring method implemented in Scanpy

https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.score_genes.html

Jasmine: Rank-based signature scoring method by Noureen et al. 2022

https://doi.org/10.7554/eLife.71994, (see signaturescoring.scoring_methods.jasmine_scoring.score_genes)

UCell: Rank-based signature scoring method by Andretta et al. 2021

https://doi.org/10.1016/j.csbj.2021.06.043, (see signaturescoring.scoring_methods.ucell_scoring.score_genes)