NEWS

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immApex 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 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 1.5.2

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

immApex 1.5.0

• Bioconductor devel branch update to match versions

immApex 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 1.3.7

UNDERLYING CHANGES

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

immApex 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 1.2.2

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

immApex 1.2.0

• Update version for BioConductor release

immApex 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 1.0.4

UNDERLYING CHANGES

• Optional testthat variationalSequences() evaluate presence of Keras

immApex 1.0.3

UNDERLYING CHANGES

• Drop evaluation of variationalSequences() example

immApex 1.0.2

UNDERLYING CHANGES

• Vignette includes eval of keras installation for certain chunks

immApex 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 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 0.99.3

UNDERLYING CHANGES

• Defining python version 3.10 for keras installation

immApex 0.99.2

UNDERLYING CHANGES

• Added discrete check and install_keras() to vignette

immApex 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