API

Import smftools as:

import smftools as smf

• Informatics: inform
• Informatics module diagram
  • smftools.informatics.bam_functions
  • smftools.informatics.basecalling
  • smftools.informatics.bed_functions
  • smftools.informatics.binarize_converted_base_identities
  • smftools.informatics.complement_base_list
  • smftools.informatics.converted_BAM_to_adata
  • smftools.informatics.fasta_functions
  • smftools.informatics.h5ad_functions
  • smftools.informatics.modkit_extract_to_adata
  • smftools.informatics.modkit_functions
  • smftools.informatics.ohe
  • smftools.informatics.pod5_functions
  • smftools.informatics.run_multiqc
  • Diagram of final steps of Direct SMF workflow
  • Diagram of final steps of Conversion SMF workflow
• Preprocessing: pp
• Preprocessing module diagram
  • smftools.preprocessing.append_base_context
  • smftools.preprocessing.append_binary_layer_by_base_context
  • smftools.preprocessing.binarize
  • smftools.preprocessing.binarize_on_Youden
  • smftools.preprocessing.binary_layers_to_ohe
  • smftools.preprocessing.calculate_complexity_II
  • smftools.preprocessing.calculate_consensus
  • smftools.preprocessing.calculate_coverage
  • smftools.preprocessing.calculate_pairwise_differences
  • smftools.preprocessing.calculate_pairwise_hamming_distances
  • smftools.preprocessing.calculate_position_Youden
  • smftools.preprocessing.calculate_read_length_stats
  • smftools.preprocessing.calculate_read_modification_stats
  • smftools.preprocessing.clean_NaN
  • smftools.preprocessing.filter_adata_by_nan_proportion
  • smftools.preprocessing.filter_reads_on_length_quality_mapping
  • smftools.preprocessing.filter_reads_on_modification_thresholds
  • smftools.preprocessing.flag_duplicate_reads
  • smftools.preprocessing.invert_adata
  • smftools.preprocessing.load_sample_sheet
  • smftools.preprocessing.make_dirs
  • smftools.preprocessing.min_non_diagonal
  • smftools.preprocessing.recipes
  • smftools.preprocessing.reindex_references_adata
  • smftools.preprocessing.subsample_adata
• Tools: tl
  • smftools.tools.calculate_umap
  • smftools.tools.cluster_adata_on_methylation
  • smftools.tools.general_tools
  • smftools.tools.position_stats
  • smftools.tools.read_stats
  • smftools.tools.spatial_autocorrelation
  • smftools.tools.subset_adata
• Analysis: an
  • Compute
  • Plot
  • Filters
  • Config
• Datasets:
  • smftools.datasets.datasets

Informatics module diagram

Preprocessing module diagram