scanpy.external¶
External API¶
Import Scanpy’s wrappers to external tools as:
import scanpy.external as sce
Preprocessing: PP¶
Batch effect correction¶
pp.bbknn(adata[, batch_key, save_knn, copy]) |
Batch balanced kNN [Park18]. |
pp.mnn_correct(*datas[, var_index, …]) |
Correct batch effects by matching mutual nearest neighbors [Haghverdi18] [Kang18]. |
Imputation¶
Note that the fundamental limitations of imputation are still under debate.
pp.dca(adata[, mode, ae_type, …]) |
Deep count autoencoder [Eraslan18]. |
pp.magic(adata[, name_list, k, a, t, n_pca, …]) |
Markov Affinity-based Graph Imputation of Cells (MAGIC) API [vanDijk18]. |
Tools: TL¶
Clustering and trajectory inference¶
tl.phenograph(data[, k, directed, prune, …]) |
PhenoGraph clustering [Levine15]. |
Gene scores, Cell cycle¶
tl.sandbag(adata, annotation, gene_names, …) |
Generate pairs of genes [Scialdone15] [Fechtner18]. |
tl.cyclone(adata, marker_pairs, gene_names, …) |
Assigns scores and predicted class to observations [Scialdone15] [Fechtner18]. |
Exporting¶
exporting.spring_project(adata, project_dir, …) |
Exports to a SPRING project directory [Weinreb17]. |
exporting.cellbrowser(adata, data_dir, data_name) |
Export adata to a UCSC Cell Browser project directory. |