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

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Documentation for package ‘immApex’ version 1.2.1

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

Help Pages

adjacencyMatrix	Adjacency matrix from amino acid or nucleotide sequences
buildNetwork	Build Edit Distance Network Using Symmetric Deletion Lookup
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