# --------------------------------------------
# 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 "Seurat" in publications use:'
type: software
license: MIT
title: 'Seurat: Tools for Single Cell Genomics'
version: 5.1.0.9005
doi: 10.1038/s41587-023-01767-y
identifiers:
- type: doi
  value: 10.32614/CRAN.package.Seurat
abstract: A toolkit for quality control, analysis, and exploration of single cell
  RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources
  of heterogeneity from single cell transcriptomic measurements, and to integrate
  diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015)
  <https://doi.org/10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <https://doi.org/10.1016/j.cell.2015.05.002>,
  Stuart T, Butler A, et al (2019) <https://doi.org/10.1016/j.cell.2019.05.031>, and
  Hao, Hao, et al (2020) <https://doi.org/10.1101/2020.10.12.335331> for more details.
authors:
- family-names: Satija
  given-names: Rahul
  email: seurat@nygenome.org
  orcid: https://orcid.org/0000-0001-9448-8833
preferred-citation:
  type: article
  title: Dictionary learning for integrative, multimodal and scalable single-cell
    analysis
  authors:
  - family-names: Hao
    given-names: Yuhan
  - family-names: Stuart
    given-names: Tim
  - family-names: Kowalski
    given-names: Madeline H
  - family-names: Choudhary
    given-names: Saket
  - family-names: Hoffman
    given-names: Paul
  - family-names: Hartman
    given-names: Austin
  - family-names: Srivastava
    given-names: Avi
  - family-names: Molla
    given-names: Gesmira
  - family-names: Madad
    given-names: Shaista
  - family-names: Fernandez-Granda
    given-names: Carlos
  - family-names: Satija
    given-names: Rahul
    email: seurat@nygenome.org
    orcid: https://orcid.org/0000-0001-9448-8833
  journal: Nature Biotechnology
  year: '2023'
  doi: 10.1038/s41587-023-01767-y
  url: https://doi.org/10.1038/s41587-023-01767-y
repository: https://mojaveazure.r-universe.dev
repository-code: https://github.com/satijalab/seurat
commit: 95de9dcf9a98c8ef1f51520abb7004f7026d0f30
url: https://satijalab.org/seurat
date-released: '2024-09-12'
contact:
- family-names: Satija
  given-names: Rahul
  email: seurat@nygenome.org
  orcid: https://orcid.org/0000-0001-9448-8833
references:
- type: article
  title: Integrated analysis of multimodal single-cell data
  authors:
  - family-names: Hao
    given-names: Yuhan
  - family-names: Hao
    given-names: Stephanie
  - family-names: Andersen-Nissen
    given-names: Erica
  - family-names: III
    given-names: William M. Mauck
  - family-names: Zheng
    given-names: Shiwei
  - family-names: Butler
    given-names: Andrew
  - family-names: Lee
    given-names: Maddie J.
  - family-names: Wilk
    given-names: Aaron J.
  - family-names: Darby
    given-names: Charlotte
  - family-names: Zagar
    given-names: Michael
  - family-names: Hoffman
    given-names: Paul
  - family-names: Stoeckius
    given-names: Marlon
  - family-names: Papalexi
    given-names: Efthymia
  - family-names: Mimitou
    given-names: Eleni P.
  - family-names: Jain
    given-names: Jaison
  - family-names: Srivastava
    given-names: Avi
  - family-names: Stuart
    given-names: Tim
  - family-names: Fleming
    given-names: Lamar B.
  - family-names: Yeung
    given-names: Bertrand
  - family-names: Rogers
    given-names: Angela J.
  - family-names: McElrath
    given-names: Juliana M.
  - family-names: Blish
    given-names: Catherine A.
  - family-names: Gottardo
    given-names: Raphael
  - family-names: Smibert
    given-names: Peter
  - family-names: Satija
    given-names: Rahul
  journal: Cell
  year: '2021'
  doi: 10.1016/j.cell.2021.04.048
  url: https://doi.org/10.1016/j.cell.2021.04.048
- type: article
  title: Comprehensive Integration of Single-Cell Data
  authors:
  - family-names: Stuart
    given-names: Tim
  - family-names: Butler
    given-names: Andrew
  - family-names: Hoffman
    given-names: Paul
  - family-names: Hafemeister
    given-names: Christoph
  - family-names: Papalexi
    given-names: Efthymia
  - family-names: III
    given-names: William M Mauck
  - family-names: Hao
    given-names: Yuhan
  - family-names: Stoeckius
    given-names: Marlon
  - family-names: Smibert
    given-names: Peter
  - family-names: Satija
    given-names: Rahul
  journal: Cell
  year: '2019'
  volume: '177'
  doi: 10.1016/j.cell.2019.05.031
  url: https://doi.org/10.1016/j.cell.2019.05.031
  start: 1888-1902
- type: article
  title: Integrating single-cell transcriptomic data across different conditions,
    technologies, and species
  authors:
  - family-names: Butler
    given-names: Andrew
  - family-names: Hoffman
    given-names: Paul
  - family-names: Smibert
    given-names: Peter
  - family-names: Papalexi
    given-names: Efthymia
  - family-names: Satija
    given-names: Rahul
  journal: Nature Biotechnology
  year: '2018'
  volume: '36'
  doi: 10.1038/nbt.4096
  url: https://doi.org/10.1038/nbt.4096
  start: 411-420
- type: article
  title: Spatial reconstruction of single-cell gene expression data
  authors:
  - family-names: Satija
    given-names: Rahul
  - family-names: Farrell
    given-names: Jeffrey A
  - family-names: Gennert
    given-names: David
  - family-names: Schier
    given-names: Alexander F
  - family-names: Regev
    given-names: Aviv
  journal: Nature Biotechnology
  year: '2015'
  volume: '33'
  doi: 10.1038/nbt.3192
  url: https://doi.org/10.1038/nbt.3192
  start: 495-502