@platforma-open/milaboratories.clonotype-convergence 1.3.1 → 1.4.1

package/block-pack/CHANGELOG.md

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+## 1.0.0
+
+Initial release.

package/block-pack/description.md

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+# Overview
+
+Detects antigen-driven clonotype convergence in B-cell receptor (BCR) repertoires using the fast-STAR statistic (Abbate et al. 2024). For each clonotype, the block counts how many other CDR3s in the same sample differ by exactly one amino acid — a per-clone neighbour density. High density signals independent B-cell lineages converging on the same CDR3 solution, a hallmark of antigen-driven selection. Outputs a Hit / Not hit flag from a configurable neighbour-frequency threshold plus the raw neighbour count and frequency, per chain. An optional cluster filter adds a stricter "binder" call: a clone is flagged when several similar CDR3s (one-edit distance) form a cluster of at least the user-set minimum size — matching the paper's headline definition.
+
+Inputs: clonotype-level VDJ data — CDR3 amino-acid sequence, CDR3 nucleotide sequence, and per-clonotype abundance. Accepts bulk Heavy, bulk Light, or single-cell BCR data; light-chain analysis on single-cell data is an explicit opt-in.
+
+**Designed for in-vivo BCR repertoires only.** In-vitro data — scFv libraries, phage / yeast display, panning-enriched repertoires — produces uninterpretable results. The algorithm runs and emits numbers, but the signal it was built to detect (germinal-center convergence under antigen-driven selection) is absent in vitro.
+
+The fast-STAR algorithm is from the Statistical Biophysics group's STAR tool. For more information, please see: [https://github.com/statbiophys/STAR](https://github.com/statbiophys/STAR) and cite the following publication if used in your research:
+
+> Abbate A. et al. Computational detection of antigen-specific B cell receptors following immunization. _PNAS_ 121(35):e2401058121 (2024). [https://doi.org/10.1073/pnas.2401058121](https://doi.org/10.1073/pnas.2401058121)

package/block-pack/manifest.json

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