External API

Warning

We are no longer accepting new tools into scanpy.external. Instead, please submit your tool to the scverse ecosystem package listing.

Note

For tools that integrate well with scanpy and anndata, see:

• The scverse ecosystem

• Scanpy’s ecosystem ecosystem page

Import Scanpy’s wrappers to external tools as:

import scanpy.external as sce

• Preprocessing: PP
  • Data integration
  • Sample demultiplexing
  • Imputation
• Tools: TL
  • Embeddings
  • Clustering and trajectory inference
  • Gene scores, Cell cycle
• Plotting: PL
  • scanpy.external.pl.phate
  • scanpy.external.pl.trimap
  • scanpy.external.pl.sam
  • scanpy.external.pl.wishbone_marker_trajectory
• Exporting
  • scanpy.external.exporting.spring_project
  • scanpy.external.exporting.cellbrowser