Tools: tl

Tools: `tl`#

`smftools.tools.calculate_knn`(adata[, obsm, ...])	Compute a KNN distance graph on an embedding in adata.obsm[obsm].
`smftools.tools.calculate_leiden`(adata, *[, ...])	Compute Leiden clusters from a connectivity graph.
`smftools.tools.calculate_nmf`(adata[, layer, ...])	Compute a low-dimensional NMF embedding.
`smftools.tools.calculate_pca`(adata[, layer, ...])	Compute PCA and store scores in .obsm and loadings in .varm.
`smftools.tools.calculate_umap`(adata[, obsm, ...])	Compute UMAP embedding from an .obsm embedding, and store connectivities.
`smftools.tools.cluster_adata_on_methylation`(...)	Add clustering groups to `adata.obs` based on methylation patterns.
`smftools.tools.general_tools`
`smftools.tools.partitioned_hmm`	Bounded HMM execution over partitioned preprocessing/spatial spines.
`smftools.tools.partitioned_spatial`	Bounded spatial analysis over partitioned preprocessing outputs.
`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`(adata, columns)	Add subset metadata based on categorical values in `.obs` or `.var` columns.
`smftools.tools.tensor_factorization`

partitioned_hmm and partitioned_spatial implement the bounded-task partitioned execution paths for the smftools hmm and smftools spatial CLI commands.