immApex

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see immApex.

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

Bioconductor version: 3.20

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 "4.4") 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")

Making Deep Learning Models with immApex HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Classification, ImmunoOncology, MotifAnnotation, Sequencing, SingleCell, Software

Version 1.0.5

In Bioconductor since BioC 3.20 (R-4.4) (< 6 months)

License MIT + file LICENSE

Depends R (>= 4.3.0)

Imports hash, httr, keras3, magrittr, matrixStats, methods, reticulate, rvest, SingleCellExperiment, stats, stringi, stringr, tensorflow, utils

System Requirements

URL https://github.com/BorchLab/immApex/

Bug Reports https://github.com/BorchLab/immApex/issues

Suggests BiocStyle, ggplot2, knitr, markdown, rmarkdown, scRepertoire, spelling, testthat, viridis

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package immApex_1.0.5.tar.gz

Windows Binary (x86_64) immApex_1.0.5.zip

macOS Binary (x86_64) immApex_1.0.0.tgz

macOS Binary (arm64) immApex_1.0.5.tgz

Source Repository git clone https://git.bioconductor.org/packages/immApex

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/immApex

Bioc Package Browser https://code.bioconductor.org/browse/immApex/

Package Short Url https://bioconductor.org/packages/immApex/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.20 Source Archive