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Ibex - Change Log

v1.1.1

  • 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

v1.0.0

  • 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
  • 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

v1.0.0

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

Pre-release Development (v0.99.6 - v0.99.31)

  • 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

Pre-release Development (v0.99.0 - v0.99.5)

  • 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