# Tools

```{eval-rst}
.. module:: BAITS.VDJ.tl
.. currentmodule:: BAITS.VDJ

.. autosummary::
    :toctree: generated

    tl.stat_clone
    tl.compute_grouped_index
    tl.aggregate_clone_df
    tl.cluster_group
    tl.process_group_with_neighbor_count
    tl.cluster_bcrs
    tl.shannon_entropy
    tl.normalize_shannon_entropy
    tl.Clonality
    tl.renyi_entropy
    tl.gini_index
    tl.Clonal_family_diversification
    tl.compute_migraIdx
    tl.calculate_clone_niche
    tl.calculate_qc_clones
    tl.calculate_qc_umis
    tl.filter_clones
    tl.filter_clones_spatial
    tl.filter_umi
    tl.filter_umi_spatial
    tl.calculate_cdr3_length
```