immApex

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

Tools for Adaptive Immune Receptor Sequence-Based Keras Modeling


Bioconductor version: Development (3.21)

A set of tools to build tensorflow/keras-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

Reference Manual PDF

Details

biocViews Annotation, Classification, ImmunoOncology, MotifAnnotation, Sequencing, SingleCell, Software
Version 1.1.0
In Bioconductor since BioC 3.20 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.3.0)
Imports hash, httr, keras, magrittr, matrixStats, methods, rvest, SingleCellExperiment, stats, stringi, stringr, tensorflow, utils
System Requirements
URL https://github.com/ncborcherding/immApex/
Bug Reports https://github.com/ncborcherding/immApex/issues
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Suggests BiocStyle, ggplot2, knitr, markdown, reticulate, rmarkdown, scRepertoire, spelling, testthat, viridis
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Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/immApex
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/immApex
Package Short Url https://bioconductor.org/packages/immApex/
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