# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "alakazam" in publications use:'
type: software
license: AGPL-3.0-only
title: 'alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis'
version: 1.4.3.999
doi: 10.1093/bioinformatics/btv359
identifiers:
- type: doi
  value: 10.32614/CRAN.package.alakazam
abstract: 'Provides methods for high-throughput adaptive immune receptor repertoire
  sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence
  lineage reconstruction, lineage topology analysis, diversity profiling, amino acid
  property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017)
  <https://doi.org/10.1093/bioinformatics/btv359>, Stern, Yaari and Vander Heiden,
  et al (2014) <https://doi.org/10.1126/scitranslmed.3008879>.'
authors:
- family-names: Marquez
  given-names: Susanna
  email: susanna.marquez@yale.edu
- family-names: Gupta
  given-names: Namita
  email: namita.gupta@yale.edu
- family-names: Nouri
  given-names: Nima
  email: nima.nouri@yale.edu
- family-names: Jiang
  given-names: Ruoyi
  email: ruoyi.jiang@yale.edu
- family-names: Zhou
  given-names: Julian
  email: julian.zhou@bulldogs.yale.edu
- family-names: Hoehn
  given-names: Kenneth
  email: kenneth.hoehn@yale.edu
- family-names: Jensen
  given-names: Cole
  email: cole.jensen@yale.edu
- family-names: Vander Heiden
  given-names: Jason
  email: jason.vanderheiden@gmail.com
- family-names: Kleinstein
  given-names: Steven
  email: steven.kleinstein@yale.edu
preferred-citation:
  type: article
  title: 'Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire
    sequencing data.'
  authors:
  - family-names: Gupta
    given-names: Namita T.
  - family-names: Vander Heiden
    given-names: Jason A.
  - family-names: Uduman
    given-names: Mohamed
  - family-names: Gadala-Maria
    given-names: Daniel
  - family-names: Yaari
    given-names: Gur
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2015'
  journal: Bioinformatics
  doi: 10.1093/bioinformatics/btv359
  start: 1-3
repository: https://immcantation.r-universe.dev
repository-code: https://github.com/immcantation/alakazam
commit: e85cde1e7f4d2b7b7750a70fe7c558d202887ff5
url: https://alakazam.readthedocs.io/
date-released: '2026-05-01'
contact:
- family-names: Marquez
  given-names: Susanna
  email: susanna.marquez@yale.edu
references:
- type: article
  title: B cells populating the multiple sclerosis brain mature in the draining cervical
    lymph nodes.
  authors:
  - family-names: Stern
    given-names: Joel N. H.
  - family-names: Yaari
    given-names: Gur
  - family-names: Vander Heiden
    given-names: Jason A.
  - family-names: Church
    given-names: George
  - family-names: Donahue
    given-names: William F.
  - family-names: Hintzen
    given-names: Rogier Q.
  - family-names: Huttner
    given-names: Anita J.
  - family-names: Laman
    given-names: Jon D.
  - family-names: Nagra
    given-names: Rashed M.
  - family-names: Nylander
    given-names: Alyssa
  - family-names: Pitt
    given-names: David
  - family-names: Ramanan
    given-names: Sriram
  - family-names: Siddiqui
    given-names: Bilal A.
  - family-names: Vigneault
    given-names: Francois
  - family-names: Kleinstein
    given-names: Steven H.
  - family-names: Hafler
    given-names: David A.
  - family-names: O'Connor
    given-names: Kevin C.
  year: '2014'
  journal: Science Translational Medicine
  issue: '248'
  volume: '6'
  doi: 10.1126/scitranslmed.3008879
  start: 248ra107