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)
Author: Nick Borcherding [aut, cre]
Maintainer: Nick Borcherding <ncborch at gmail.com>
citation("immGLIPH")):
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")
## 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/immGLIPH/ |
| Package Short Url | https://bioconductor.org/packages/immGLIPH/ |
| Package Downloads Report | Download Stats |