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.fastq_export
- smftools.informatics.h5ad_functions
- smftools.informatics.modkit_extract_to_adata
- smftools.informatics.modkit_functions
- smftools.informatics.ohe
- smftools.informatics.partition_read
- smftools.informatics.partition_store
- smftools.informatics.pod5_functions
- smftools.informatics.ragged_store
- smftools.informatics.raw_store
- smftools.informatics.reference_identity
- smftools.informatics.run_multiqc
- smftools.informatics.sequence_encoding
- smftools.informatics.sidecar_manifest
- smftools.informatics.signal_features
- smftools.informatics.storage_planner
- 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.append_mismatch_frequency_sites
- smftools.preprocessing.append_sequence_mismatch_annotations
- smftools.preprocessing.append_variant_call_layer
- 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_cigar_indels
- 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.label_deaminase_pcr_chimeras
- smftools.preprocessing.load_sample_sheet
- smftools.preprocessing.make_dirs
- smftools.preprocessing.min_non_diagonal
- smftools.preprocessing.partitioned_executor
- smftools.preprocessing.preprocess_umi_annotations
- smftools.preprocessing.recipes
- smftools.preprocessing.reindex_references_adata
- smftools.preprocessing.subsample_adata
- smftools.preprocessing.umi_bipartite_analysis
- Tools:
tl- smftools.tools.calculate_knn
- smftools.tools.calculate_leiden
- smftools.tools.calculate_nmf
- smftools.tools.calculate_pca
- smftools.tools.calculate_umap
- smftools.tools.cluster_adata_on_methylation
- smftools.tools.general_tools
- smftools.tools.partitioned_hmm
- smftools.tools.partitioned_spatial
- smftools.tools.position_stats
- smftools.tools.read_stats
- smftools.tools.rolling_nn_distance
- smftools.tools.sequence_alignment
- smftools.tools.spatial_autocorrelation
- smftools.tools.subset_adata
- smftools.tools.tensor_factorization
- Analysis:
an - Plotting:
pl- smftools.plotting.autocorrelation_plotting
- smftools.plotting.chimeric_plotting
- smftools.plotting.classifiers
- smftools.plotting.general_plotting
- smftools.plotting.hmm_plotting
- smftools.plotting.latent_plotting
- smftools.plotting.plotting_utils
- smftools.plotting.pod5_plotting
- smftools.plotting.position_stats
- smftools.plotting.preprocess_plotting
- smftools.plotting.qc_plotting
- smftools.plotting.spatial_plotting
- smftools.plotting.umi_plotting
- smftools.plotting.variant_plotting
- Datasets:
Informatics module diagram#
Preprocessing module diagram#
