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

## Documentation for package ‘immApex’ version 1.7.0

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

## Help Pages

ace_richness | ACE Richness Estimator
adjacencyMatrix | Adjacency Matrix From Amino Acid or Nucleotide Sequences
amino.acids | Standard 20 amino acids
buildNetwork | Build Edit Distance Network
calculateEntropy | Positional Entropy / Diversity Biological Sequences
calculateFrequency | Relative Residue Frequencies at Every Position
calculateGeneUsage | Quantifcation of Gene-Locus Usage
calculateMotif | Motif Enumeration and Counting
calculateProperty | Position-wise Amino-Acid Property Profiles
chao1_richness | Chao1 Richness Estimator
d50_dom | D50 Dominance Index
dxx_dom | Dxx Dominance Index
formatGenes | Ensure clean gene nomenclature using IMGT annotations
generateSequences | Randomly Generate Amino Acid Sequences
geometricEncoder | Universal Amino-acid Sequence Encoder
getIMGT | Get IMGT Sequences for Specific Loci
getIR | Extract Immune Receptor Sequences
gini_coef | Gini Coefficient of Abundance Inequality
gini_simpson | Gini–Simpson Diversity
hill_q | Hill-Number Generator
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 CDR-loop segments from V-gene calls
inv_simpson | Inverse Simpson Diversity
mutateSequences | Randomly Mutate Sequences of Amino Acids
norm_entropy | Normalised Shannon Entropy
onehotEncoder | Universal Amino-acid Sequence Encoder
pielou_evenness | Pielou’s Evenness
positionalEncoder | Generate Sinusoidal Positional Encodings
probabilityMatrix | Position Probability Matrix for Amino Acid or Nucleotide Sequences
propertyEncoder | Universal Amino-acid Sequence Encoder
scaleMatrix | Fast Matrix Scaling or Transformation
sequenceDecoder | Decode Amino Acid or Nucleotide Sequences
sequenceEncoder | Universal Amino-acid Sequence Encoder
shannon_entropy | Shannon Diversity Index (Entropy)
summaryMatrix | Fast Matrix Summaries
tokenizeSequences | Generate Tokenized Sequences from Amino Acid String