Changes in version 1.3.7                        

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

                        Changes in version 1.2.2                        

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

                        Changes in version 1.2.0                        

  - Update version for BioConductor release

                        Changes in 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

                        Changes in version 1.0.4                        

UNDERLYING CHANGES

  - Optional testthat variationalSequences() evaluate presence of Keras

                        Changes in version 1.0.3                        

UNDERLYING CHANGES

  - Drop evaluation of variationalSequences() example

                        Changes in version 1.0.2                        

UNDERLYING CHANGES

  - Vignette includes eval of keras installation for certain chunks

                        Changes in 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

                       Changes in 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

                       Changes in version 0.99.3                        

UNDERLYING CHANGES

  - Defining python version 3.10 for keras installation

                       Changes in version 0.99.2                        

UNDERLYING CHANGES

  - Added discrete check and install_keras() to vignette

                       Changes in 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