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Releases: BorchLab/immApex

immApex 1.5.3

03 Apr 12:36
@github-actions github-actions
v1.5.3
ac82a8c

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immApex 1.5.3 Latest
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Release of immApex version 1.5.3.

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Version 1.4.0

31 Oct 12:52
@ncborcherding ncborcherding
1.4.0
b2a3afb

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Version 1.4.0

immApex VERSION 1.3.6

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
  • dded summaryMatrix() for fast summarization of matrix values

DEPRCATED FEATURES

  • Defunct variationalSequences()

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)
  • Robust checks before running getIMGT() for website functioning
  • Improved speed of generateSequences(), mutateSequences(), adjacencyMatrix(), tokenizeSequences(), geometricEncoder()
  • Added group.by argument to getIR()
  • Removed python-based dependencies
  • Reduce overall dependencies on external packages
  • Updated C++ backend to C++17
  • Updated unit tests and vignette check

BUGS

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