Grouping of Lymphocyte Interactions by Paratope Hotspots

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Documentation for package ‘immGLIPH’ version 0.99.5

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

clusterScoring	Score CDR3 clusters using the GLIPH or GLIPH2 algorithm
deNovoTCRs	Generate de novo TCR sequences
findMotifs	Find continuous and discontinuous sequence motifs
getGLIPHreference	Get or download the immGLIPH reference list
getRandomSubsample	Draw a stratified random subsample from the reference repertoire
gliph_input_data	Example TCR input data
gliph_sce	Example SingleCellExperiment with TCR clonal information
gTRB	Germline TCR-beta CDR3 fragments
loadGLIPH	Load saved GLIPH results from disk
plotNetwork	Visualize TCR convergence group network
reference_list	GLIPH reference repertoire list (external data)
ref_cluster_sizes	Cluster size probabilities in naive reference repertoire
runGLIPH	Run the GLIPH or GLIPH2 TCR clustering algorithm