scglue.data

Auxiliary functions for anndata.AnnData objects that are not covered in scanpy.

Functions

`aggregate_obs`	Aggregate obs in a given dataset by certain categories
`aggregate_var`	Aggregate var in a given dataset by certain categories
`bedmap2anndata`	Convert bedmap result to `anndata.AnnData` object
`calc_hypo_score`	Calculates the hypo-methylation score as X based on methylated counts and total coverage stored in separate layers
`count_prep`	Standard preprocessing of count-based dataset with total count normalization and log-transformation
`estimate_balancing_weight`	Estimate balancing weights in an unsupervised manner
`extract_rank_genes_groups`	Extract result of `scanpy.tl.rank_genes_groups()` in the form of marker gene data frame for specific cell groups
`get_gene_annotation`	Get genomic annotation of genes by joining with a GTF file.
`get_metacells`	Aggregate datasets into metacells
`lsi`	LSI analysis (following the Seurat v3 approach)
`merge_mc_cov`
`metacell_corr`	Metacell based correlation
`metacell_regr`	Metacell-based regression
`transfer_labels`	Transfer discrete labels from reference dataset to query dataset

Classes