Tools

tl.stat_clone(df, groupby, Cgene_col, clone_col)	Compute the number of unique clones per group and optionally plot.
tl.compute_grouped_index(df, group_by, ...)	Compute a diversity index (e.g., Shannon entropy) per group.
tl.aggregate_clone_df(df, group_by, ...[, ...])	Aggregate clone counts and frequencies per group.
tl.cluster_group(cdr3_list[, threshold])	Cluster a list of CDR3 nucleotide sequences based on sequence identity.
tl.process_group_with_neighbor_count(group)	Process a grouped BCR dataframe to assign clusters and neighbor counts.
tl.cluster_bcrs(igh_df[, threshold, ...])	Cluster BCR sequences across an entire dataset and compute neighbor degrees.
tl.shannon_entropy(p)	Compute Shannon entropy of a probability vector.
tl.normalize_shannon_entropy(p)	Compute normalized Shannon entropy (range 0-1).
tl.Clonality(p)	Compute clonality metric from Shannon entropy.
tl.renyi_entropy(probabilities[, alpha_values])	Calculate the Rényi entropy for a given probability distribution and alpha.
tl.gini_index(data)	Compute Gini index of a distribution.
tl.Clonal_family_diversification(df[, ...])	Compute clonal family diversification (Gini index of clone sizes per sample).
tl.compute_migraIdx(df[, sample_col, ...])	Compute migration index between spatial clusters for BCR clones.
tl.calculate_clone_niche(df, sample, ...[, ...])	Calculate spatial niche composition around a target BCR clone.
tl.calculate_qc_clones(df, group_by, ...[, ...])	Compute per-group clone counts and per-spatial-location clone counts.
tl.calculate_qc_umis(df, group_by, ...[, ...])	Compute per-group and per-spatial-location UMI counts for clones.
tl.filter_clones(df, clone_col[, min_clone])	Filter dataframe by minimum clone count.
tl.filter_clones_spatial(df, clone_spatial_col)	Filter dataframe by minimum spatial clone count.
tl.filter_umi(df, umi_key[, min_umi])	Filter dataframe by minimum UMI count per clone.
tl.filter_umi_spatial(df, clone_umi_key[, ...])	Filter dataframe by minimum spatial UMI count per clone.
tl.calculate_cdr3_length(df, sample_col, ...)	Calculate the CDR3 length for each clone and optionally plot the distribution.