immGLIPH
This is the development version of immGLIPH; to use it, please install the devel version of Bioconductor.
Grouping of Lymphocyte Interactions by Paratope Hotspots
Bioconductor version: Development (3.24)
An R implementation of the GLIPH and GLIPH2 algorithms for clustering T cell receptors (TCRs) predicted to bind the same HLA-restricted peptide antigen. Identifies specificity groups based on local (motif-based) and global (sequence-based) CDR3 similarities. Integrates with the scRepertoire ecosystem via immApex for single-cell immune repertoire analysis. Users should cite the original GLIPH algorithm papers: Glanville et al. (2017) <doi:10.1038/nature22976> and Huang et al. (2020) <doi:10.1038/s41587-020-0505-4>.
Author: Nick Borcherding [aut, cre]
Maintainer: Nick Borcherding <ncborch at gmail.com>
citation("immGLIPH")):Nick Borcherding. immGLIPH: Grouping of Lymphocyte Interactions by Paratope Hotspots. doi:10.18129/B9.bioc.immGLIPH, R package version 0.99.5, https://bioconductor.org/packages/immGLIPH.
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("immGLIPH")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("immGLIPH")| Getting Started with immGLIPH | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, ImmunoOncology, Sequencing, SingleCell, Software, Visualization |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | stringdist, igraph, BiocParallel, parallel, stringr, stats, utils, graphics, grDevices, viridis, visNetwork, plotfunctions, immApex |
| System Requirements | |
| URL | https://github.com/BorchLab/immGLIPH https://github.com/BorchLab/scRepertoire https://github.com/BorchLab/immApex |
| Bug Reports | https://github.com/BorchLab/immGLIPH/issues |
See More
| Suggests | BiocFileCache, scRepertoire, SeuratObject, Seurat, SingleCellExperiment, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| 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 | immGLIPH_0.99.5.tar.gz |
| Windows Binary (x86_64) | immGLIPH_0.99.5.zip |
| macOS Binary (big-sur-x86_64) | immGLIPH_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | immGLIPH_0.99.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/immGLIPH |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/immGLIPH |
| Package Short Url | https://bioconductor.org/packages/immGLIPH/ |
| Package Downloads Report | Download Stats |