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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "immGLIPH" in publications use:'
type: software
license: MIT
title: 'immGLIPH: Grouping of Lymphocyte Interactions by Paratope Hotspots'
version: 0.99.5
doi: 10.1038/nature22976
identifiers:
- type: url
  value: https://github.com/BorchLab/immApex
abstract: '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) <https://doi.org/10.1038/nature22976> and Huang et al. (2020)
  <https://doi.org/10.1038/s41587-020-0505-4>.'
authors:
- family-names: Borcherding
  given-names: Nick
  email: ncborch@gmail.com
preferred-citation:
  type: article
  title: Identifying specificity groups in the T cell receptor repertoire
  authors:
  - family-names: Glanville
    given-names: Jacob
  - family-names: Huang
    given-names: Huang
  - family-names: Nau
    given-names: Allison
  - family-names: Hatber
    given-names: Olivia
  - family-names: Patel
    given-names: Reshma
  - family-names: Arendt
    given-names: David
  - family-names: Pinilla
    given-names: Clemencia
  - family-names: Houghten
    given-names: Richard
  - family-names: Gifford
    given-names: David
  - family-names: Steinman
    given-names: Ralf
  - family-names: Davis
    given-names: Mark
  journal: Nature
  year: '2017'
  volume: '547'
  doi: 10.1038/nature22976
  start: '94'
  end: '98'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/BorchLab/immGLIPH
commit: 17636de1dcad06e64a93a739d88bf90eb2d41c83
url: https://github.com/BorchLab/scRepertoire
date-released: '2026-05-20'
contact:
- family-names: Borcherding
  given-names: Nick
  email: ncborch@gmail.com
references:
- type: article
  title: Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor
    clustering with GLIPH2 and genome-wide antigen screening
  authors:
  - family-names: Huang
    given-names: Huang
  - family-names: Wang
    given-names: Chunlin
  - family-names: Rubelt
    given-names: Florian
  - family-names: Scriba
    given-names: Thomas
  - family-names: Davis
    given-names: Mark
  journal: Nature Biotechnology
  year: '2020'
  volume: '38'
  doi: 10.1038/s41587-020-0505-4
  start: '1194'
  end: '1202'