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ravibandaru-lab merged 1 commit into from
Jul 23, 2026
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docs: document the Miller-Madow correction added to regional-mds #189

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11 changes: 8 additions & 3 deletions docs/documentation/user_guide/features.rst
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Expand Up @@ -59,9 +59,14 @@ Motif Diversity Score (MDS)
MDS (*Jiang et al. 2020*) is the normalized Shannon entropy of the end-motif
k-mer distribution, summarizing end-motif diversity in a single number. The
regional Motif Diversity Score (rMDS) computes that same entropy per genomic
region (*Bandaru et al. 2026*).

:Commands: ``mds`` (whole sample), ``regional-mds`` (per region)
region (*Bandaru et al. 2026*). Because the underlying plug-in entropy
estimator is biased downward in regions with few fragments, ``regional-mds``
accepts an optional ``--miller-madow`` flag that applies a Miller-Madow bias
correction, making rMDS values comparable across regions of differing depth.
It is off by default, so existing output is unchanged unless requested.

:Commands: ``mds`` (whole sample), ``regional-mds`` (per region, optionally
bias-corrected with ``--miller-madow``)

Cleavage profile
----------------
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6 changes: 5 additions & 1 deletion docs/documentation/workflow/index.rst
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Expand Up @@ -179,7 +179,11 @@ Each command's options below carry the FinaleToolkit flag they map to. Optional
(``--strand``: ``both``, ``forward``, or ``reverse``), ``*_mapq`` (``-q``),
``*_workers`` (``-t``).

**mds** / **regional-mds**: ``*_sep`` (``-s``), ``*_header`` (``--header``).
**mds**: ``mds_sep`` (``-s``), ``mds_header`` (``--header``).

**regional-mds**: ``regional_mds_sep`` (``-s``), ``regional_mds_header``
(``--header``), ``regional_mds_miller_madow`` (``--miller-madow``;
Miller-Madow bias correction, off by default).

**wps**: ``wps_site_bed`` (positional REGIONS), ``wps_reference`` (``-r``),
``wps_chrom_sizes`` (``--chrom-sizes``), ``wps_interval_size`` (``-i``),
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