NEWS

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Ibex 1.1.1

• Aligned version with Bioconductor release
• Switched default branch to devel for Bioconductor compatibility
• Updated CI workflows to target devel branch
• Converted NEWS to NEWS.md format
• Added automated GitHub Release workflow via tags
• Ibex_matrix() now accepts character vectors of amino acid sequences directly
• Removed rlang from Imports, added lifecycle
• As per basilisk documentation:
  • Add .BBSoptions with UnsupportedPlatforms: win32
  • Add configure and configure.win scripts
• Add Docker infrastructure with Dockerfile and .devcontainer/devcontainer.json
• Improved testthat compatibility across platforms
• Improve adherence to verbosity arguments

Ibex 1.0.0

Major Underlying Changes

• Integration of Ibex with immApex
• Updated Seurat object to v5
• Runs using basilisk instead of reticulate - no installation of python packages

Feature Changes

• Renamed Ibex.matrix() to Ibex_matrix()
• Updated support for SCE format for runIbex()
• Update CoNGAfy() to function with all versions of Seurat
• Updated quietBCRgenes() to use VariableFeatures() call for SeuratV5 and backward compatibility
• Add getHumanIgPseudoGenes() to return a list of human Immunoglobulin Pseudo genes that are kept by quietBCRgenes()

New Models

• Added New Light and Heavy Chain Models
• Encoding methods now accepted: "OHE", "atchleyFactors", "crucianiProperties", "kideraFactors", "MSWHIM", "tScales", "zScales"
• Sequence input:
  • Human Heavy: 10000000
  • Human Light: 5000000
  • Human Heavy-Expanded: 5000000
  • Human Light-Expanded: 2500000
  • Mouse Heavy: 5000000
  • Mouse Heavy-Expanded: 5000000
• Trained convolutional and variational autoencoders for Heavy/Light chains
  • Architecture: 512-256-128-256-512
  • Parameters:
    • Batch Size = 128
    • Latent Dimensions = 128
    • Epochs = 100
    • Loss = Mean Squared Error (CNN) & KL Divergence (VAE)
    • Activation = relu
    • Learning rate = 1e-6
  • Optimizers: Adam
  • Early stopping was set to patients of 10 for minimal validation loss and restoration of best weights
  • CNN autoencoders have batch normalization layers between the dense layers

Ibex 0.99.31

• ibex_ensure_basilisk_external_dir no longer importsFrom basilisk.utils directly
• Moved data processing script out of vignette to inst/scripts
• Added ibex_ensure_basilisk_external_dir with basilisk.utils
• Adding internal .OnLoad() function to handle basilisk lock dir issue
• Deprecated quietBCRgenes()
• Converted Ibex.matrix() to Ibex_matrix()
• Added Install Instructions for Bioconductor on README and Vignette
• Removed references to Keras3 Installation

Ibex 0.99.5

• Initial commit and early development
• Added detection of chain length to function call
• Added support for direct output of combineBCR()
• Modified quietBCR() to include constant regions and J-chains
• Updated models to include radam optimization, early stop, trained on 800,000 unique cdr3s
• quietBCRgenes() now does not remove human Ig pseudogenes
• Updated models for manuscript revision
• Added chain.checker() function to allow for uncapitalized chain calls
• Trained classical and variational autoencoders for light/heavy chains (architecture: 256-128-30-128-256)
• Integration of Ibex with immApex
• Updated Seurat object to v5
• Updated support for SCE format for runIbex()
• Update CoNGAfy() to function with all versions of Seurat
• Updated quietBCRgenes() to use VariableFeatures() call for SeuratV5 and backward compatibility
• Added getHumanIgPseudoGenes() to return a list of human Immunoglobulin Pseudo genes
• Added new light and heavy chain models with encoding methods: OHE, atchleyFactors, crucianiProperties, kideraFactors, MSWHIM, tScales, zScales
• Trained convolutional and variational autoencoders (architecture: 512-256-128-256-512)
• Implementing GitHub action workflows
• Adding testthat framework
• Deprecated clonalCommunity
• Added geometric encoding using the BLOSUM62 matrix
• Added information to example data
• Examples now check if python is installed and running
• Updated example data to 2k HEL BEAM-Ab from 10x
• Converted ibex_example into SCE object for compliance
• Large revision of vignette to fit new data/format
• Added species argument to runIbex
• Implementing GitHub action workflows
• Adding testthat framework
• Deprecating clonalCommunity
• Added geometric encoding using the BLOSUM62 matrix
• Added chain.checker() function to allow for uncapitalized chain calls
• Updated models for manuscript revision
• Updated models to include radam optimization, early stop, trained on 800,000 unique cdr3s
• quietBCRgenes() now does not remove human Ig pseudogenes
• Added detection of chain length to function call
• Added support for direct output of combineBCR()
• Modified quietBCR() to include constant regions and J-chains
• Initial commit
• Deprecated quietBCRgenes()
• Converted Ibex.matrix() to Ibex_matrix()
• Added Install Instructions for Bioconductor on README and Vignette
• Removed references to Keras3 Installation
• Moved data processing script out of vignette to inst/scripts
• Added ibex_ensure_basilisk_external_dir with basilisk.utils
• Adding internal .OnLoad() function to handle basilisk lock dir issue