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immApex VERSION 1.7.1

PERFORMANCE

buildNetwork() now scales to large, clonally expanded repertoires. The C++ engine was rewritten around candidate generation instead of all-pairs comparison, with no new dependencies and identical edge output for the default settings:

  • Identical sequences collapse to one representative before any distance is computed, so clonal expansion no longer drives quadratic work.
  • Length and V/J blocking act as an index. Only length-compatible representatives in the same block are compared.
  • Levenshtein and Damerau use deletion-neighborhood (SymSpell) hashing for small edit distances, with Damerau indexed at radius 2k. Hamming uses pigeonhole segment indexing. Both fall back to length-blocked comparison outside their range.
  • Edges accumulate as integer node indices and gain their labels in R, which avoids building millions of barcode strings inside the parallel core.

Speedups range from roughly 2x on mixed repertoires with many V genes to about 70x when one block holds many unique sequences at a tight threshold.

NEW FEATURES

  • Added the expand argument to buildNetwork(). "clique" (default) materializes every pairwise edge and reproduces the exact edge multiplicity that community-detection clustering expects. "star" links identical sequences through a single hub and connects related groups hub to hub. "star" produces far fewer edges and preserves connected components exactly, so it is a large memory win when the downstream step depends on connectivity.

BUG FIXES

  • Fixed a banded Levenshtein error that dropped pairs whose only optimal alignment rides the band edge, including identical sequences at a tight normalized threshold. The boundary cell read the wrong diagonal value. The fix only recovers true edges and never removes valid ones.
  • Made the normalized-threshold cutoff robust to floating-point rounding so a normalized distance exactly equal to the threshold is kept, matching the documented inclusive behavior.

immApex VERSION 1.5.4

BUG FIXES

  • Fixed vignette build failure when IMGT network data is unavailable (e.g., on Bioconductor build servers)
  • Fixed operator precedence bug in inferCDR() reference validation check

immApex VERSION 1.5.3

UNDERLYING CHANGES

  • getIMGT() now uses immReferent as a backend for downloading and caching IMGT reference sequences
  • Removed frame, max.retries, and verbose parameters from getIMGT()
  • Added refresh parameter to getIMGT() for controlling cache behavior
  • Removed hash, httr, and rvest package dependencies (now handled by immReferent)
  • Replaced .parseSpecies() with .mapSpecies() for immReferent species name compatibility

immApex VERSION 1.5.2

  • improved error message for the propertyEncoder() function when the suggested Peptides package is not installed.

immApex VERSION 1.5.0

  • Bioconductor devel branch update to match versions

immApex VERSION 1.4.3

NEW FEATURES

The buildNetwork() function has been significantly enhanced to include:

  • Multiple distance metrics: Added support for five distance metrics via the dist_type parameter:

    • "levenshtein" (default): Standard edit distance
    • "hamming": Substitutions only (requires equal-length sequences)
    • "damerau": Levenshtein with transpositions
    • "nw": Needleman-Wunsch global alignment
    • "sw": Smith-Waterman local alignment

  • Flexible normalization: New normalize parameter supports three modes:

    • "none" (default): Raw distance values (backward compatible)
    • "maxlen": Normalize by max(length(seq1), length(seq2))
    • "length": Normalize by mean sequence length

immApex VERSION 1.3.7

UNDERLYING CHANGES

  • Ensure buildNetwork() returns a symmetric distance matrix and drops nonstructural zeros

immApex VERSION 1.3.6

UNDERLYING CHANGES

  • Rebuilt propertyEncoder() and onehotEncoder() to use C++ backend with encodeSequences.cpp
  • Rebuilt buildNetwork() via C++ integration (fastEditEdges.cpp)
  • Motif quantification in calculateMotif() use C++ (calculateMotif.cpp)
  • Reduce overall dependencies on external packages
  • Improved speed of generateSequences(), mutateSequences(), adjacencyMatrix(), tokenizeSequences(), geometricEncoder
  • Added group.by argument to getIR()
  • Defunct variationalSequences()
  • Removed keras3/tensorflow suggests/dependencies
  • Removed baslisk environment, python no longer required
  • Updated C++ backend to C++17
  • Robust checks before running getIMGT() for website functioning
  • Removing special unicode symbols

NEW FEATURES

  • calculateEntropy() added to calculate the positional entropy along a biological sequence
  • Added basic diversity metrics (exported) to support calculateEntropy()
  • calculateFrequency() added to calculate the positional frequency along a biological sequence
  • calculateMotif() added to get motif quantification of sequences
  • calculateGeneUsage() added for single/paired gene enumeration
  • Added scaleMatrix() for comprehensive scale/transformation functions
  • Added summaryMatrix() for fast summarization of matrix values

BUGS

  • Fixed NT position issue with inferCDR()
  • Fixed generateSequence() range issue for single-length sequences
  • Fixed binary frequency issue in positionalEncoder()
  • Fixed buildNetwork() for relative thresholding returns relative value

immApex VERSION 1.2.2

  • Updated unit tests and vignette check
  • Converted package to basilisk from reticulate

immApex VERSION 1.2.0

  • Update version for BioConductor release

immApex VERSION 1.0.5

UNDERLYING CHANGES

  • getIMGT() checks for availability of IMGT website
  • Expanded Unit Tests
  • Unit Tests and Vignette now evaluate for proper python installation overall

immApex VERSION 1.0.4

UNDERLYING CHANGES

  • Optional testthat variationalSequences() evaluate presence of Keras

immApex VERSION 1.0.3

UNDERLYING CHANGES

  • Drop evaluation of variationalSequences() example

immApex VERSION 1.0.2

UNDERLYING CHANGES

  • Vignette includes eval of keras installation for certain chunks

immApex VERSION 1.0.1

UNDERLYING CHANGES

  • Fix issue with optimizer call in variationalSequences()
  • Move package to keras3
  • Version Bump to be consistent with Bioconductor release

immApex VERSION 0.99.5

UNDERLYING CHANGES

  • Remove keras installation in vignette
  • Removed lazydata loading
  • Added @return to the data manual entries
  • Update stop message for propertyEncoder()
  • Removed set.seed from variationalSequences()
  • Added runnable example for variationalSequences()
  • Added better handling of no connection in getIMGT()
  • Added max.retries to getIMGT()
  • Updated testthat for new IMGT version

immApex VERSION 0.99.3

UNDERLYING CHANGES

  • Defining python version 3.10 for keras installation

immApex VERSION 0.99.2

UNDERLYING CHANGES

  • Added discrete check and install_keras() to vignette

immApex VERSION 0.99.1

UNDERLYING CHANGES

  • Added warning to getIMGT() to mention IMGT license on first use
  • import magrittr instead of dplyr
  • Fixed issue with license error
  • Added example to positionalEncoder()
  • Replaced discrete calling of "es =" in vignette
  • Update readme to include keras based installation
  • added set.seed() to vignette
  • added introduction section to vignette with mention of other packages
  • removed installation section from vignette (can't add BioC instructions until accepted)
  • Fixed rendering issue with the vignette
  • Subsampled example data and removed Omniscope example
  • Updated testthat for formatGenes() and inferCDR() for new example data
  • Reduced size of test data
  • Minimized usage of sapply() and X:Y per BiocCheck suggestions
  • Modified print() messages to messages()
  • Add verbose parameter to turn on/off processing steps
  • Added links for example data formats