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Bioconductor - immApex (development version)

immApex

This is the development version of immApex; for the stable release version, see immApex.

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

Bioconductor version: Development (3.22)

A set of tools to build tensorflow/keras3-based models 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.

Author: Nick Borcherding [aut, cre]

Maintainer: Nick Borcherding <ncborch at gmail.com>

Citation (from within R, enter citation("immApex")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("immApex")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("immApex")
Details biocViews Annotation, Classification, ImmunoOncology, MotifAnnotation, Sequencing, SingleCell, Software Version 1.3.0 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) License MIT + file LICENSE Depends R (>= 4.3.0) Imports hash, httr, igraph, keras3, magrittr, matrixStats, methods, Rcpp (>= 0.12.11), reticulate, rvest, SingleCellExperiment, stats, stringi, stringr, tensorflow, utils System Requirements URL https://github.com/BorchLab/immApex/ Bug Reports https://github.com/BorchLab/immApex/issues See More Suggests BiocStyle, ggraph, ggplot2, knitr, graph, markdown, rmarkdown, scRepertoire, spelling, testthat, tidygraph, viridis Linking To Rcpp Enhances Depends On Me Imports Me scRepertoire Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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