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Version 1.2.0: Feb 2026

MAJOR CHANGES:

• Leiden Community Detection: Added support for Leiden algorithm as an alternative to hierarchical clustering. Use clustering_method = "leiden" in inferAlleleClusters(). This is particularly useful for D and J segments with variable-length sequences.

• Generalized Distance Functions: The new igDistance() function supports multiple distance calculation methods:

  • “decipher”: DECIPHER-based distance (default, best for aligned V segments)
  • “hamming”: Hamming distance (requires equal-length sequences)
  • “lv”: Levenshtein distance (handles variable-length sequences, good for D/J)

• Multi-locus Support: inferAlleleClusters() now explicitly supports all V/D/J segments with the locus parameter.

• New Visualization Functions:

  • plotTruncatedTree(): Publication-quality circular tree with collapsed subgroups
  • plotCommunityNetwork(): Network visualization of cluster relationships
  • plotSilhouetteOptimization(): Resolution parameter optimization plot
  • plotClusterComparison(): Compare hierarchical and Leiden clustering results

CLASS SYSTEM CHANGES:

• S4 to S3 Migration: GermlineCluster is now an S3 class instead of S4.
  • Access slots with $ instead of @ (e.g., result$alleleClusterTable)
  • Added print(), summary(), and plot() S3 methods
  • New slots: clusteringMethod, communityObject, graphObject, distanceMatrix, silhouetteScore, resolutionParameter, locus

API CHANGES:

• ighvDistance() is deprecated in favor of igDistance() (backward compatible wrapper provided)
• ighvClust() is deprecated in favor of igClust() (backward compatible wrapper provided)
• inferAlleleClusters() has new parameters but maintains backward compatibility

DEPENDENCIES:

• Added: igraph, stringdist, cluster, ape
• Moved to Suggests: ComplexHeatmap, dplyr, ggtree
• Removed from Imports: dplyr (replaced with data.table operations)

MINOR CHANGES:

• Improved CRAN compliance with proper Author and Maintainer fields
• Added test suite using testthat (edition 3)
• Redesigned Shiny app with modular architecture
• Added Conda recipe for bioconda distribution

BUG FIXES:

• Fixed deprecated dplyr::between() calls
• Fixed deprecated dplyr::bind_rows() calls
• Replaced deprecated S4 slot access patterns

Version 1.0.7: Mar 19, 2025

• Working version for CRAN.

Version 1.0.6: Nov 7, 2024

• An asc_annotation flag was added to inferGenotypeAllele to simplify genotype by asc annotation.

Version 1.0.5: Oct 1, 2024

• New Feature! We added a confidence level to genotype inference genotype_confidence.

The confidence is calculated as the Z score of the allele count, repertoire depth, and the allele absolute threshold.

Version 1.0.4: April 24, 2024

• Fixed bug in download_zenodo_files.

Version 1.0.3: December 13, 2023

• Fixed bug in download_zenodo_files.

Version 1.0.1: September 13, 2023

• Fixed bug in download_zenodo_files.

Version 1.0.1: August 16, 2023

• First CRAN release.

Version 1.0.0: June 9, 2023

• First release.

Version 0.0.1: December 7, 2022

• Stable version.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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