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

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DOI: 10.18129/B9.bioc.immApex

Bioconductor version: Release (3.22)

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")

Machine and 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 1.4.0

In Bioconductor since BioC 3.20 (R-4.4) (1 year)

License MIT + file LICENSE

Depends R (>= 4.3.0)

Imports hash, httr, Matrix, matrixStats, methods, Rcpp, rvest, SingleCellExperiment, stats, stringr, utils

System Requirements Python (via basilisk)

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

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

Suggests BiocStyle, dplyr, ggraph, ggplot2, igraph, knitr, markdown, Peptides, randomForest, rmarkdown, scRepertoire, spelling, testthat, tidygraph, viridis

Linking To Rcpp

Enhances

Depends On Me

Imports Me Ibex, scRepertoire

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package immApex_1.4.0.tar.gz

Windows Binary (x86_64) immApex_1.4.0.zip

macOS Binary (x86_64) immApex_1.4.0.tgz

macOS Binary (arm64) immApex_1.4.0.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/

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