# Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning

## Documentation for package ‘immApex’ version 1.0.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

adjacencyMatrix | Adjacency matrix from amino acid or nucleotide sequences
formatGenes | Ensure clean gene nomenclature using IMGT annotations
generateSequences | Randomly Generate Amino Acid Sequences
geometricEncoder | Geometric Encoder from Amino Acid Strings
getIMGT | Get IMGT Sequences for Specific Loci
getIR | Extract Immune Receptor Sequences
immapex_AA.data | A list of amino acid properties
immapex_blosum.pam.matrices | List of amino acid substitution matrices
immapex_example.data | Example contig data for Apex
immapex_gene.list | A list of IMGT gene names by genes, loci, and species
inferCDR | Infer portions of the CDR Loop from Vgene data
mutateSequences | Randomly Mutate Sequences of Amino Acids
onehotEncoder | One Hot Encoder from Amino Acid or Nucleotide Strings
positionalEncoder | Adding Position-Specific Information to Sequences
probabilityMatrix | Position Probability Matrix for Amino Acid or Nucleotide Sequences
propertyEncoder | Encoder from Amino Acid String by Properties
sequenceDecoder | One Hot Decoder from One Hot Encoded Matrix or 3D Array
tokenizeSequences | Generate Tokenized Sequences from Amino Acid String
variationalSequences | Generate Similar Sequences using Variational Autoencoder