DESCRIPTION

Package: Trex
Title: Methods for TCR single-cell embedding 
Version: 0.99.12
Date: 2024-10-08
Authors@R: c(
    person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"),
    person(given = "Drew", family = "Voigt", role = c("aut"), email = "drewvoigt@gmail.com"))
Description: Implementation of the Trex algorithm for single-cell embedding based on TCR sequences. The package includes a standalone function to encode TCR sequence information by amino acid properties or sequence order using tensorflow-based autoencoder. In addition, the package interacts with SingleCellExperiment or Seurat data objects. 
License: MIT + file LICENSE 
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.3.2
biocViews: Software, ImmunoOncology, SingleCell, Classification, Annotation, Sequencing
Depends: 
	R (>= 4.0)
Imports: stringr, 
	SeuratObject,
	SingleCellExperiment,
	rlang,
	keras,
	tensorflow,
	reticulate, 
	Matrix, 
	matrixStats,
	SummarizedExperiment,
        stats,
	stringdist, 
	utils
Suggests: 
	knitr, 
	rmarkdown, 
	dplyr,
	markdown,
	BiocStyle,  
	Seurat,
	viridis,
	patchwork,
	ggplot2,
	spelling,
        testthat (>= 3.0.0)
VignetteBuilder: knitr
Language: en-US
URL: https://github.com/ncborcherding/Trex/
BugReports: https://github.com/ncborcherding/Trex/issues