smftools.preprocessing.append_base_context(adata)
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Append base context annotations to adata. |
smftools.preprocessing.append_binary_layer_by_base_context(...)
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Build per-reference masked layers for base-context sites. |
smftools.preprocessing.binarize
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smftools.preprocessing.binarize_on_Youden(adata)
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Binarize SMF values using thresholds from calculate_position_Youden. |
smftools.preprocessing.binary_layers_to_ohe
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smftools.preprocessing.calculate_complexity_II(adata)
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Estimate and optionally plot library complexity. |
smftools.preprocessing.calculate_consensus
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smftools.preprocessing.calculate_coverage(adata)
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Append position-level coverage metadata per reference category. |
smftools.preprocessing.calculate_pairwise_differences
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smftools.preprocessing.calculate_pairwise_hamming_distances
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smftools.preprocessing.calculate_position_Youden(adata)
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Add position-level Youden thresholds and optional ROC plots. |
smftools.preprocessing.calculate_read_length_stats(adata)
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Calculate per-read length statistics and store them in adata.obs. |
smftools.preprocessing.calculate_read_modification_stats(...)
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Add methylation/deamination statistics for each read. |
smftools.preprocessing.clean_NaN(adata[, ...])
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Append layers to adata that contain NaN-cleaning strategies. |
smftools.preprocessing.filter_adata_by_nan_proportion(...)
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Filter an AnnData object on NaN proportion in a matrix axis. |
smftools.preprocessing.filter_reads_on_length_quality_mapping(adata)
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Filter AnnData by coordinates, read length, quality, and mapping metrics. |
smftools.preprocessing.filter_reads_on_modification_thresholds(...)
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Filter reads based on per-read modification thresholds. |
smftools.preprocessing.flag_duplicate_reads(...)
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Flag duplicate reads with demux-aware keeper preference. |
smftools.preprocessing.invert_adata(adata[, ...])
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Invert the AnnData object along the column axis in-place. |
smftools.preprocessing.load_sample_sheet(...)
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Load a sample sheet CSV and map metadata into adata.obs. |
smftools.preprocessing.make_dirs
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smftools.preprocessing.min_non_diagonal
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smftools.preprocessing.recipes
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smftools.preprocessing.reindex_references_adata(adata)
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Reindex genomic coordinates by adding per-reference offsets. |
smftools.preprocessing.subsample_adata(adata)
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Subsample an AnnData object by observation categories. |
