API reference

This page gives an overview of all public snapatac2 objects, functions and methods.

• Input/Output
  • Backed AnnData objects
  • AnnData IO
• Preprocessing: pp
  • BAM/Fragment file processing
  • Matrix operation
  • Doublet removal
  • Data Integration
• Tools: tl
  • Embeddings
  • Clustering
  • Peak calling
  • Differential analysis
  • Motif analysis
  • Network analysis (beta)
  • Utilities
• Metrics
  • Quality Control
• Plotting: pl
  • snapatac2.pl.tsse
  • snapatac2.pl.umap
  • snapatac2.pl.motif_enrichment
  • snapatac2.pl.regions
  • snapatac2.pl.spectral_eigenvalues
  • snapatac2.pl.network_edge_stat
  • snapatac2.pl.render_plot
• Exporting: ex
  • snapatac2.ex.export_fragments
  • snapatac2.ex.export_coverage
• Datasets
  • Genomes
  • Motifs
  • Raw data