# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "shazam" in publications use:'
type: software
license: AGPL-3.0-only
title: 'shazam: Immunoglobulin Somatic Hypermutation Analysis'
version: 1.2.1.999
doi: 10.1093/bioinformatics/btv359
identifiers:
- type: doi
  value: 10.32614/CRAN.package.shazam
abstract: 'Provides a computational framework for analyzing mutations in immunoglobulin
  (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection
  pressure, mutational load quantification, building of somatic hypermutation (SHM)
  models, and model-dependent distance calculations. Also includes empirically derived
  models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al
  (2015) <https://doi.org/10.1093/bioinformatics/btv359>, Yaari, et al (2012) <https://doi.org/10.1093/nar/gks457>,
  Yaari, et al (2013) <https://doi.org/10.3389/fimmu.2013.00358>, Cui, et al (2016)
  <https://doi.org/10.4049/jimmunol.1502263>.'
authors:
- family-names: Uduman
  given-names: Mohamed
  email: mohamed.uduman@yale.edu
- family-names: Gupta
  given-names: Namita
  email: namita.gupta@yale.edu
- family-names: Marquez
  given-names: Susanna
  email: susanna.marquez@yale.edu
- family-names: Zhou
  given-names: Julian
  email: julian.zhou@yale.edu
- family-names: Nouri
  given-names: Nima
  email: nima.nouri@yale.edu
- family-names: Yann Lee
  given-names: Noah
  email: noah.yann.lee@yale.edu
- family-names: Vander Heiden
  given-names: Jason
  email: jason.vanderheiden@gmail.com
- family-names: Yaari
  given-names: Gur
  email: gur.yaari@biu.ac.il
- 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
    email: mohamed.uduman@yale.edu
  - family-names: Gadala-Maria
    given-names: Daniel
  - family-names: Yaari
    given-names: Gur
    email: gur.yaari@biu.ac.il
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2015'
  journal: Bioinformatics
  doi: 10.1093/bioinformatics/btv359
  start: 1-3
repository: https://ssnn-airr.r-universe.dev
repository-code: https://bitbucket.org/kleinstein/shazam
commit: 563e3b6d8922c0561ca03cd80fc0184b4fc04b9a
url: http://shazam.readthedocs.io
date-released: '2024-08-01'
contact:
- family-names: Marquez
  given-names: Susanna
  email: susanna.marquez@yale.edu
references:
- type: article
  title: Quantifying selection in high-throughput Immunoglobulin sequencing data sets.
  authors:
  - family-names: Yaari
    given-names: Gur
  - family-names: Uduman
    given-names: Mohamed
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2012'
  journal: Nucleic acids research
  volume: '40'
  issue: '17'
  doi: 10.1093/nar/gks457
  start: e134
- type: article
  title: Models of somatic hypermutation targeting and substitution based on synonymous
    mutations from high-throughput immunoglobulin sequencing data.
  authors:
  - family-names: Yaari
    given-names: Gur
  - family-names: Vander Heiden
    given-names: Jason A.
  - family-names: Uduman
    given-names: Mohamed
  - family-names: Gadala-Maria
    given-names: Daniel
  - family-names: Gupta
    given-names: Namita T.
  - family-names: Stern
    given-names: Joel N. H.
  - family-names: O'Connor
    given-names: Kevin C.
  - family-names: Hafler
    given-names: David A.
  - family-names: Lasserson
    given-names: Uri
  - family-names: Vigneault
    given-names: Francois
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2013'
  journal: Frontiers in Immunology
  volume: '4'
  issue: '358'
  doi: 10.3389/fimmu.2013.00358
  start: 1-11
- type: article
  title: A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput
    Ig Sequencing Data.
  authors:
  - family-names: Cui
    given-names: Ang
  - family-names: Di Niro
    given-names: Roberto
  - family-names: Vander Heiden
    given-names: Jason A.
  - family-names: Briggs
    given-names: Adrian W.
  - family-names: Adams
    given-names: Kris
  - family-names: Gilbert
    given-names: Tamara
  - family-names: O'Connor
    given-names: Kevin C.
  - family-names: Vigneault
    given-names: Francois
  - family-names: Shlomchik
    given-names: Mark J.
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2016'
  journal: The Journal of Immunology
  volume: '197'
  issue: '9'
  doi: 10.4049/jimmunol.1502263
  start: 3566-3574
- type: article
  title: Optimized Threshold Inference for Partitioning of Clones From High-Throughput
    B Cell Repertoire Sequencing Data
  authors:
  - family-names: Nouri
    given-names: Nima
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2018'
  journal: Frontiers in Immunology
  volume: '9'
  doi: 10.3389/fimmu.2018.01687