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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/immApex/ |
| Package Short Url | https://bioconductor.org/packages/immApex/ |
| Package Downloads Report | Download Stats |