immApex

immApex provides tools for machine and deep learning in R from amino acid and nucleotide sequences focusing on adaptive immune receptors.

Key Features:

• Sequence Pre-processing: Prepares amino acid and nucleotide sequences for downstream analysis.
• Gene Nomenclature Unification: Standardizes gene nomenclature usage across datasets.
• Sequence Encoding: Converts sequences into formats suitable for machine and deep learning models.
• Model Combination: Enables integration and combination of multiple models.
• scRepertoire Compatibility: Serves as the basis for immune receptor sequence functions, packages, and models compatible with the scRepertoire ecosystem.

Scientific Applications:

• Adaptive Immune Receptor Analysis: Supports machine and deep learning workflows applied to adaptive immune receptor sequences.
• Single-Cell Immune Repertoire Integration: Provides foundational tools for future immune receptor sequence analysis within the scRepertoire ecosystem.

Methodology:

The package implements sequence pre-processing, gene nomenclature unification, sequence encoding, and model combination methods in R.