# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "scRepertoire" in publications use:'
type: software
license: MIT
title: 'scRepertoire: A toolkit for single-cell immune receptor profiling'
version: 2.8.0
doi: 10.1371/journal.pcbi.1012760
identifiers:
- type: doi
  value: 10.32614/CRAN.package.scRepertoire
abstract: scRepertoire is a toolkit for processing and analyzing single-cell T-cell
  receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use
  of 10x, AIRR, BD, MiXCR, TRUST4, and WAT3R single-cell formats. The functionality
  includes basic clonal analyses, repertoire summaries, distance-based clustering
  and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R
  single-cell workflows.
authors:
- family-names: Borcherding
  given-names: Nick
  email: ncborch@gmail.com
- family-names: Yang
  given-names: Qile
  email: qile.yang@berkeley.edu
- family-names: Safina
  given-names: Ksenia
  email: safina@broadinstitute.org
preferred-citation:
  type: article
  title: 'ScRepertoire 2: Enhanced and efficient toolkit for single-cell immune profiling'
  authors:
  - family-names: Yang
    given-names: Qile
    email: qile.yang@berkeley.edu
  - family-names: Safina
    given-names: Ksenia R.
  - family-names: Nguyen
    given-names: Kieu Diem Quynh
  - family-names: Tuong
    given-names: Zeweb Kelvin
  - family-names: Borcherding
    given-names: Nicholas
  journal: PLOS Computational Biology
  doi: 10.1371/journal.pcbi.1012760
  year: '2025'
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/BorchLab/scRepertoire
commit: fa0190a78833ec4f1ae1124948bc1f6c027bd4c2
url: https://www.borch.dev/uploads/scRepertoire/
date-released: '2026-04-28'
contact:
- family-names: Borcherding
  given-names: Nick
  email: ncborch@gmail.com
references:
- type: article
  title: 'scRepertoire: An R-based toolkit for single-cell immune receptor analysis'
  authors:
  - family-names: Borcherding
    given-names: Nicholas
  - family-names: Bormann
    given-names: Nicholas L
  - family-names: Kraus
    given-names: Gloria
  journal: F1000Research
  volume: '9'
  year: '2022'
  publisher:
    name: Faculty of 1000 Ltd
  doi: 10.12688/f1000research.22139.2
  url: https://doi.org/10.12688/f1000research.22139.2