sccross.models.sccross.SCCROSSModel.perturbation_difGenes

SCCROSSModel.perturbation_difGenes(key, adata, obs_key, perturb_key, reference_key, genes, use_rep='X_pca', rep_dim=100)[source]

Obtain differential genes generated by perturbation

Parameters

  • key (str) – Domain key

  • adata (AnnData) – Input dataset

  • obs_key (str) – Obs name we use to identify cells

  • perturb_key (str) – Name of cells we would like to perturb

  • reference_key (str) – Name of cells we regard as reference

  • genes ([]) – Genes we would like to perturb

  • use_rep (str) – Name of representation used by this data

  • rep_dim (int) – Dimension of representation used by this data

  • batch_size – Size of minibatches

Return type

DataFrame

Returns

pd.DataFrame – Genes with their bias with shape \(n_{gene} \times n_{3}\)