Package: immApex 1.7.0

Nick Borcherding

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

A set of tools to for machine and deep learning in R from amino acid and nucleotide sequences focusing on adaptive immune receptors. The package includes pre-processing of sequences, unifying gene nomenclature usage, encoding sequences, and combining models. This package will serve as the basis of future immune receptor sequence functions/packages/models compatible with the scRepertoire ecosystem.

Authors:Nick Borcherding [aut, cre, cph], Qile Yang [ctb]

immApex_1.7.0.tar.gz
immApex_1.7.0.zip(r-4.7)immApex_1.7.0.zip(r-4.6)immApex_1.7.0.zip(r-4.5)
immApex_1.7.0.tgz(r-4.6-x86_64)immApex_1.7.0.tgz(r-4.6-arm64)immApex_1.7.0.tgz(r-4.5-x86_64)immApex_1.7.0.tgz(r-4.5-arm64)
immApex_1.7.0.tar.gz(r-4.7-arm64)immApex_1.7.0.tar.gz(r-4.7-x86_64)immApex_1.7.0.tar.gz(r-4.6-arm64)immApex_1.7.0.tar.gz(r-4.6-x86_64)
immApex_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
immApex/json (API)
NEWS

# Install 'immApex' in R:

install.packages('immApex', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/borchlab/immapex/issues

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

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

On BioConductor:immApex-1.7.0(bioc 3.24)immApex-1.6.0(bioc 3.23)

software immunooncology singlecell classification annotation sequencing motifannotation cpp openmp

7.18 score 14 stars 3 packages 12 scripts 505 downloads 36 exports 46 dependencies

Last updated from:92dbbf33ac. Checks:1 WARNING, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	298
linux-devel-arm64	OK	270
linux-devel-x86_64	OK	301
source / vignettes	OK	287
linux-release-arm64	OK	321
linux-release-x86_64	OK	362
macos-release-arm64	OK	290
macos-release-x86_64	OK	394
macos-oldrel-arm64	OK	204
macos-oldrel-x86_64	OK	362
windows-devel	OK	614
windows-release	OK	298
windows-oldrel	OK	635
wasm-release	OK	147

Exports:ace_richness adjacencyMatrix amino.acids buildNetwork calculateEntropy calculateFrequency calculateGeneUsage calculateMotif calculateProperty chao1_richness d50_dom dxx_dom formatGenes generateSequences geometricEncoder getIMGT getIR gini_coef gini_simpson hill_q inferCDR inv_simpson mutateSequences norm_entropy onehotEncoder pielou_evenness positionalEncoder probabilityMatrix propertyEncoder scaleMatrix sequenceDecoder sequenceEncoder shannon_entropy summaryMatrix tokenizeSequences variationalSequences

Dependencies:abind askpass Biobase BiocGenerics Biostrings cli crayon curl DelayedArray generics GenomicRanges glue httr immReferent IRanges jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig R6 Rcpp rlang rvest S4Arrays S4Vectors selectr Seqinfo SingleCellExperiment SparseArray stringi stringr SummarizedExperiment sys tibble utf8 vctrs xml2 XVector yaml

Machine and Deep Learning Models with immApex

Nick Borcherding

Rendered fromimmApex.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-04-03
Started: 2024-08-05

Citation

Development and contributors

Readme and manuals

Help Manual

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