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Bioconductor - immApex

immApex

This is the released version of immApex; for the devel version, see immApex.

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

Bioconductor version: Release (3.21)

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.

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")

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 1.2.5 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) License MIT + file LICENSE Depends R (>= 4.3.0) Imports basilisk, hash, httr, keras3, magrittr, matrixStats, methods, rvest, SingleCellExperiment, stats, stringi, stringr, tensorflow, utils System Requirements Python (via basilisk) URL https://github.com/BorchLab/immApex/ Bug Reports https://github.com/BorchLab/immApex/issues See More Suggests BiocStyle, ggraph, ggplot2, knitr, ggraph, rmarkdown, scRepertoire, spelling, testthat, tidygraph, viridis Linking To Enhances Depends On Me Imports Me 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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