API

Preprocessing

pp.load_vcf(vcf_path[, show_progress, ...])	Load a VCF file into an AnnData object.
pp.annotate_contexts(adata, fasta_path[, ...])	Annotate variants with trinucleotide contexts.
pp.filter_variants(adata[, min_cells, ...])	Filter variants based on presence across cells/samples.
pp.filter_cells(adata[, min_variants, ...])	Filter cells/samples based on number of variants detected.
pp.filter_by_coverage(adata, min_depth[, ...])	Filter variants based on sequencing depth (coverage) across cells/samples.
pp.filter_to_snps(adata[, chrom_prefix, inplace])	Filter to only single nucleotide variants (SNPs).

Tools

tl.compute_spectrum(adata[, count_strategy, ...])	Compute 96-channel mutation spectrum for each cell/sample or per private mutation group.
tl.compute_callable_sites(adata, min_depth)	Compute the number of callable sites per cell/sample.
tl.normalize_spectrum(adata, key[, method, ...])	Normalize a mutation spectrum by various strategies.
tl.private_mutations(adata[, groupby, ...])	Identify mutations that are private (unique) to each cell/sample or group.

Plotting

pl.spectrum(adata[, key, cells, groupby, ...])	Plot mutation spectra for cells/samples or per-group private mutations.
pl.spectrum_from_df(spectrum_df[, ...])	Plot mutation spectrum directly from a DataFrame.
pl.compare_spectra(adata, keys[, aggregate, ...])	Compare multiple spectra (e.g., different filtering strategies or conditions).