API

import tfmindi as tm

• Preprocessing pp
  • tfmindi.pp.extract_seqlets
  • tfmindi.pp.calculate_motif_similarity
  • tfmindi.pp.create_seqlet_adata
• Tools tl
  • tfmindi.tl.cluster_seqlets
  • tfmindi.tl.create_patterns
  • tfmindi.tl.run_topic_modeling
  • tfmindi.tl.evaluate_topic_models
• Plotting pl
  • tfmindi.pl.tsne
  • tfmindi.pl.tsne_logos
  • tfmindi.pl.dbd_heatmap
  • tfmindi.pl.dbd_topic_heatmap
  • tfmindi.pl.region_contributions
  • tfmindi.pl.dbd_logos
  • tfmindi.pl.dbd_cluster_logos
  • tfmindi.pl.region_topic_tsne
  • tfmindi.pl.render_plot
• Input/Output
  • tfmindi.save_h5ad
  • tfmindi.load_h5ad
  • tfmindi.save_patterns
  • tfmindi.load_patterns
• Datasets
  • tfmindi.fetch_motif_collection
  • tfmindi.fetch_motif_annotations
  • tfmindi.load_motif_collection
  • tfmindi.load_motif_annotations
  • tfmindi.load_motif_to_dbd
• Types
  • Pattern
  • Seqlet
• Backends
  • tfmindi.get_backend
  • tfmindi.set_backend
  • tfmindi.is_gpu_available
• Merge
  • tfmindi.concat