Introduction | Installation | Loading Package | Integration with the scRepertoire Ecosystem | Quick Start | Loading the Example Data | Input Data Format | Working with Single-Cell Data | The runGLIPH() Function | Key Arguments | Method Presets | Running GLIPH2 (Default) | Running GLIPH1 | Understanding the Output | Cluster Properties | Cluster Membership | Motif Enrichment | Network Edges | Customizing the Analysis | Using method = "custom" | Adjusting Significance Thresholds | Choosing a Reference Database | Using a Custom Reference Database | Motif Discovery with findMotifs() | Example | Cluster Scoring with clusterScoring() | Scoring Components | De Novo TCR Generation with deNovoTCRs() | Network Visualization with plotNetwork() | Loading Saved Results with loadGLIPH() | Saving Results to Disk | Performance | Accelerated Computation with immApex | Tips and Best Practices | Session Info
Package: immGLIPH 0.99.5
Nick Borcherding
immGLIPH: Grouping of Lymphocyte Interactions by Paratope Hotspots
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>.
Authors:
immGLIPH_0.99.5.tar.gz
immGLIPH_0.99.5.zip(r-4.7)immGLIPH_0.99.5.zip(r-4.6)immGLIPH_0.99.5.zip(r-4.5)
immGLIPH_0.99.5.tgz(r-4.6-any)immGLIPH_0.99.5.tgz(r-4.5-any)
immGLIPH_0.99.5.tar.gz(r-4.7-any)immGLIPH_0.99.5.tar.gz(r-4.6-any)
immGLIPH_0.99.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
immGLIPH/json (API)
| # Install 'immGLIPH' in R: |
| install.packages('immGLIPH', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/borchlab/immgliph/issues
Datasets:
- gliph_input_data - Example TCR input data
- gliph_sce - Example SingleCellExperiment with TCR clonal information
- gTRB - Germline TCR-beta CDR3 fragments
- ref_cluster_sizes - Cluster size probabilities in naive reference repertoire
On BioConductor:immGLIPH-0.99.5(bioc 3.24)
softwareimmunooncologyclusteringsinglecellsequencingvisualization
Last updated from:17636de1dc. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 210 | ||
| linux-devel-x86_64 | OK | 279 | ||
| source / vignettes | OK | 288 | ||
| linux-release-x86_64 | OK | 337 | ||
| macos-release-arm64 | OK | 159 | ||
| macos-oldrel-arm64 | OK | 108 | ||
| windows-devel | OK | 162 | ||
| windows-release | OK | 150 | ||
| windows-oldrel | OK | 152 | ||
| wasm-release | OK | 221 |
Exports:clusterScoringdeNovoTCRsfindMotifsgetGLIPHreferencegetRandomSubsampleloadGLIPHplotNetworkrunGLIPH
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbslibcachemclicodetoolscpp11crayoncurlDelayedArraydigestevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrigraphimmApeximmReferentIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplotfunctionsR6rappdirsRColorBrewerRcpprlangrmarkdownrvestS4ArraysS4VectorsS7sassscalesselectrSeqinfoSingleCellExperimentsnowSparseArraystringdiststringistringrSummarizedExperimentsystibbletinytexutf8vctrsviridisviridisLitevisNetworkwithrxfunxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Score CDR3 clusters using the GLIPH or GLIPH2 algorithm | clusterScoring |
| Generate de novo TCR sequences | deNovoTCRs |
| Find continuous and discontinuous sequence motifs | findMotifs |
| Get or download the immGLIPH reference list | getGLIPHreference |
| Draw a stratified random subsample from the reference repertoire | getRandomSubsample |
| Example TCR input data | gliph_input_data |
| Example SingleCellExperiment with TCR clonal information | gliph_sce |
| Germline TCR-beta CDR3 fragments | gTRB |
| Load saved GLIPH results from disk | loadGLIPH |
| Visualize TCR convergence group network | plotNetwork |
| Cluster size probabilities in naive reference repertoire | ref_cluster_sizes |
| GLIPH reference repertoire list (external data) | reference_list |
| Run the GLIPH or GLIPH2 TCR clustering algorithm | runGLIPH |
