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# CITATION.cff 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 "ECLIPSE" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'ECLIPSE: Enhanced CLonotypic Inference via Prediction of Single-cell Expression'
version: 0.99.3
doi: 10.64898/2026.02.18.706444
abstract: This package is used for the analysis of single-cell T cell receptor sequencing
  data (scTCR-seq). ECLIPSE maps chain pairings across a sample to predict the true
  clonotype of each cell, unlike other methods which only consider the chains that
  are sequenced in each cell. Seurat/SingleCellExperiment objects and Cell Ranger
  vdj/multi contig files are required as inputs.
authors:
- family-names: Burns
  given-names: Ethan
  email: ethan.burns@yale.edu
  orcid: https://orcid.org/0009-0009-8061-3686
- family-names: Braun
  given-names: David
  email: david.braun@yale.edu
  orcid: https://orcid.org/0000-0003-4543-5553
preferred-citation:
  type: article
  title: VDJdive and ECLIPSE enhance single-cell T cell receptor sequencing analysis
    through the probabilistic resolution of ambiguous clonotypes
  authors:
  - family-names: Burns
    given-names: Ethan C.
  - family-names: Movassagh
    given-names: Mercedeh
  - family-names: Lundell
    given-names: Jill F.
  - family-names: Ye
    given-names: Mingzhi
  - family-names: Ye
    given-names: Zhaochen
  - family-names: Oliveira
    given-names: Giacomo
  - family-names: Rout
    given-names: Rishabh
  - family-names: Hugaboom
    given-names: Miya B.
  - family-names: Street
    given-names: Kelly
  - family-names: Braun
    given-names: David A.
  journal: bioRxiv
  year: '2026'
  doi: 10.64898/2026.02.18.706444
repository: https://bioc.r-universe.dev
repository-code: https://github.com/eburns10/ECLIPSE
commit: 9ca87aa15bb1338cdc909abde5bd9569c1ebf15f
url: https://github.com/eburns10/ECLIPSE
date-released: '2026-11-10'
contact:
- family-names: Burns
  given-names: Ethan
  email: ethan.burns@yale.edu
  orcid: https://orcid.org/0009-0009-8061-3686