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 (3.23)
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, cph], Qile Yang [ctb] 
Maintainer: Nick Borcherding <ncborch at gmail.com>
citation("immApex")):Nick Borcherding. immApex: Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning. doi:10.18129/B9.bioc.immApex, R package version 1.6.0, https://bioconductor.org/packages/immApex.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, Classification, ImmunoOncology, MotifAnnotation, Sequencing, SingleCell, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | immReferent, Matrix, matrixStats, methods, Rcpp, SingleCellExperiment, stats, stringr, utils |
| System Requirements | |
| URL | https://github.com/BorchLab/immApex/ |
| Bug Reports | https://github.com/BorchLab/immApex/issues |
See More
| 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, immLynx, scRepertoire |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | immApex_1.6.0.tar.gz |
| Windows Binary (x86_64) | immApex_1.6.0.zip |
| macOS Binary (big-sur-x86_64) | immApex_1.6.0.tgz |
| macOS Binary (sonoma-arm64) | immApex_1.6.0.tgz |
| 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/ |
| Package Downloads Report | Download Stats |