CITATION.cff

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "SCOT" in publications use:'
type: software
license: MIT
title: 'SCOT: Single Cell Omics Toolbox'
version: 0.0.0.9000
abstract: Toolbox for single cell RNA-seq.
authors:
- family-names: Wong
  given-names: Nathan
  email: nathan.wong@nih.gov
- family-names: Sovacool
  given-names: Kelly
  email: kelly.sovacool@nih.gov
  orcid: https://orcid.org/0000-0003-3283-829X
- family-names: Koparde
  given-names: Vishal
  email: vishal.koparde@nih.gov
  orcid: https://orcid.org/0000-0001-8978-8495
contact:
- family-names: Wong
  given-names: Nathan
  email: nathan.wong@nih.gov
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: 'R Foundation for Statistical Computing (ROR: <https://ror.org/05qewa988>)'
    address: Vienna, Austria
  year: '2026'
  doi: 10.32614/R.manuals
  version: '>= 4.1.0'
- type: software
  title: AnnotationDbi
  abstract: 'AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor'
  notes: Imports
  url: https://bioconductor.org/packages/AnnotationDbi
  repository: https://bioconductor.org/
  authors:
  - family-names: Pagès
    given-names: Hervé
  - family-names: Carlson
    given-names: Marc
  - family-names: Falcon
    given-names: Seth
  - family-names: Li
    given-names: Nianhua
  year: '2026'
  doi: 10.18129/B9.bioc.AnnotationDbi
- type: software
  title: AUCell
  abstract: 'AUCell: AUCell: Analysis of ''gene set'' activity in single-cell RNA-seq
    data (e.g. identify cells with specific gene signatures)'
  notes: Imports
  url: http://scenic.aertslab.org
  repository: https://bioconductor.org/
  authors:
  - family-names: Aibar
    given-names: Sara
  - family-names: Leuven
    given-names: Stein Aerts. Laboratory of Computational Biology. VIB-KU Leuven Center
      for Brain & Disease Research.
  - name: Belgium.
  year: '2026'
  doi: 10.18129/B9.bioc.AUCell
- type: software
  title: BiocGenerics
  abstract: 'BiocGenerics: S4 generic functions used in Bioconductor'
  notes: Imports
  url: https://bioconductor.org/packages/BiocGenerics
  repository: https://bioconductor.org/
  authors:
  - name: The Bioconductor Dev Team
  - family-names: Pagès
    given-names: Hervé
    email: hpages.on.github@gmail.com
    orcid: https://orcid.org/0009-0002-8272-4522
  year: '2026'
  doi: 10.18129/B9.bioc.BiocGenerics
- type: software
  title: celldex
  abstract: 'celldex: Index of Reference Cell Type Datasets'
  notes: Imports
  url: https://support.bioconductor.org/
  repository: https://bioconductor.org/
  authors:
  - family-names: Aran
    given-names: Dvir
    email: dvir.aran@ucsf.edu
  - family-names: Lun
    given-names: Aaron
    email: infinite.monkeys.with.keyboards@gmail.com
  - family-names: Bunis
    given-names: Daniel
  - family-names: Andrews
    given-names: Jared
    email: jared.andrews07@gmail.com
  - family-names: Dündar
    given-names: Friederike
    email: frd2007@med.cornell.edu
  year: '2026'
  doi: 10.18129/B9.bioc.celldex
- type: software
  title: clusterSim
  abstract: 'clusterSim: Searching for Optimal Clustering Procedure for a Data Set'
  notes: Imports
  repository: https://CRAN.R-project.org/package=clusterSim
  authors:
  - family-names: Walesiak
    given-names: Marek
    email: marek.walesiak@ue.wroc.pl
    orcid: https://orcid.org/0000-0003-0922-2323
  - family-names: Dudek
    given-names: Andrzej
    email: andrzej.dudek@ue.wroc.pl
    orcid: https://orcid.org/0000-0002-4943-8703
  year: '2026'
  doi: 10.32614/CRAN.package.clusterSim
- type: software
  title: djvdj
  abstract: 'djvdj: A collection of single-cell V(D)J tools'
  notes: Imports
  url: https://rnabioco.github.io/djvdj/
  repository: https://bioconductor.org/
  authors:
  - family-names: Sheridan
    given-names: Ryan
    email: ryan.sheridan@cuanschutz.edu
    orcid: https://orcid.org/0000-0003-4012-3147
  year: '2026'
- type: software
  title: DoubletFinder
  abstract: 'DoubletFinder: DoubletFinder is a suite of tools for identifying doublets
    in single-cell RNA sequencing data'
  notes: Imports
  authors:
  - name: c)
  - name: person
  - name: c
  year: '2026'
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2026'
  doi: 10.32614/CRAN.package.dplyr
- type: software
  title: DropletUtils
  abstract: 'DropletUtils: Utilities for Handling Single-Cell Droplet Data'
  notes: Imports
  repository: https://bioconductor.org/
  authors:
  - family-names: Lun
    given-names: Aaron
  year: '2026'
  doi: 10.18129/B9.bioc.DropletUtils
- type: software
  title: flexmix
  abstract: 'flexmix: Flexible Mixture Modeling'
  notes: Imports
  repository: https://CRAN.R-project.org/package=flexmix
  authors:
  - family-names: Gruen
    given-names: Bettina
    email: Bettina.Gruen@R-project.org
    orcid: https://orcid.org/0000-0001-7265-4773
  - family-names: Leisch
    given-names: Friedrich
    orcid: https://orcid.org/0000-0001-7278-1983
  year: '2026'
  doi: 10.32614/CRAN.package.flexmix
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Imports
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  - family-names: Brand
    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2026'
  doi: 10.32614/CRAN.package.ggplot2
- type: software
  title: ggpubr
  abstract: 'ggpubr: ''ggplot2'' Based Publication Ready Plots'
  notes: Imports
  url: https://rpkgs.datanovia.com/ggpubr/
  repository: https://CRAN.R-project.org/package=ggpubr
  authors:
  - family-names: Kassambara
    given-names: Alboukadel
    email: alboukadel.kassambara@gmail.com
  year: '2026'
  doi: 10.32614/CRAN.package.ggpubr
- type: software
  title: ggrepel
  abstract: 'ggrepel: Automatically Position Non-Overlapping Text Labels with ''ggplot2'''
  notes: Imports
  url: https://ggrepel.slowkow.com/
  repository: https://CRAN.R-project.org/package=ggrepel
  authors:
  - family-names: Slowikowski
    given-names: Kamil
    email: kslowikowski@gmail.com
    orcid: https://orcid.org/0000-0002-2843-6370
  year: '2026'
  doi: 10.32614/CRAN.package.ggrepel
- type: software
  title: glue
  abstract: 'glue: Interpreted String Literals'
  notes: Imports
  url: https://glue.tidyverse.org/
  repository: https://CRAN.R-project.org/package=glue
  authors:
  - family-names: Hester
    given-names: Jim
    orcid: https://orcid.org/0000-0002-2739-7082
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2026'
  doi: 10.32614/CRAN.package.glue
- type: software
  title: grDevices
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: 'R Foundation for Statistical Computing (ROR: <https://ror.org/05qewa988>)'
    address: Vienna, Austria
  year: '2026'
  doi: 10.32614/R.manuals
- type: software
  title: harmony
  abstract: 'harmony: Fast, Sensitive, and Accurate Integration of Single Cell Data'
  notes: Imports
  url: https://pati-ni.github.io/harmony/
  repository: https://CRAN.R-project.org/package=harmony
  authors:
  - family-names: Patikas
    given-names: Nikolaos
    email: nik.patik@gmail.com
    orcid: https://orcid.org/0000-0002-3978-0134
  - family-names: Yao
    given-names: Hongcheng
    email: hongchengyaonk@gmail.com
    orcid: https://orcid.org/0000-0002-0743-4835
  - family-names: Korsunsky
    given-names: Ilya
    email: ilya.korsunsky@gmail.com
    orcid: https://orcid.org/0000-0003-4848-3948
  - family-names: Hemberg
    given-names: Martin
    email: mhemberg@bwh.harvard.edu
    orcid: https://orcid.org/0000-0001-8895-5239
  - family-names: Millard
    given-names: Nghia
    email: nmillard@g.harvard.edu
    orcid: https://orcid.org/0000-0002-0518-7674
  - family-names: Fan
    given-names: Jean
    email: jeanfan@fas.harvard.edu
    orcid: https://orcid.org/0000-0002-0212-5451
  - family-names: Slowikowski
    given-names: Kamil
    email: kslowikowski@gmail.com
    orcid: https://orcid.org/0000-0002-2843-6370
  - family-names: Raychaudhuri
    given-names: Soumya
    orcid: https://orcid.org/0000-0002-1901-8265
  year: '2026'
  doi: 10.32614/CRAN.package.harmony
- type: software
  title: magrittr
  abstract: 'magrittr: A Forward-Pipe Operator for R'
  notes: Imports
  url: https://magrittr.tidyverse.org
  repository: https://CRAN.R-project.org/package=magrittr
  authors:
  - family-names: Bache
    given-names: Stefan Milton
    email: stefan@stefanbache.dk
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.magrittr
- type: software
  title: ontoProc
  abstract: 'ontoProc: processing of ontologies of anatomy, cell lines, and so on'
  notes: Imports
  url: https://github.com/vjcitn/ontoProc
  repository: https://bioconductor.org/
  authors:
  - family-names: Carey
    given-names: Vincent
    email: stvjc@channing.harvard.edu
    orcid: https://orcid.org/0000-0003-4046-0063
  year: '2026'
  doi: 10.18129/B9.bioc.ontoProc
- type: software
  title: org.Hs.eg.db
  abstract: 'org.Hs.eg.db: Genome wide annotation for Human'
  notes: Imports
  repository: https://bioconductor.org/
  authors:
  - family-names: Carlson
    given-names: Marc
  year: '2026'
- type: software
  title: org.Mm.eg.db
  abstract: 'org.Mm.eg.db: Genome wide annotation for Mouse'
  notes: Imports
  repository: https://bioconductor.org/
  authors:
  - family-names: Carlson
    given-names: Marc
  year: '2026'
- type: software
  title: Orthology.eg.db
  abstract: 'Orthology.eg.db: Orthology mapping package'
  notes: Imports
  repository: https://bioconductor.org/
  authors:
  - family-names: Carlson
    given-names: Marc
  year: '2026'
- type: software
  title: reshape2
  abstract: 'reshape2: Flexibly Reshape Data: A Reboot of the Reshape Package'
  notes: Imports
  url: https://github.com/hadley/reshape
  repository: https://CRAN.R-project.org/package=reshape2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.reshape2
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.rlang
- type: software
  title: rliger
  abstract: 'rliger: Linked Inference of Genomic Experimental Relationships'
  notes: Imports
  url: https://welch-lab.github.io/liger/
  repository: https://CRAN.R-project.org/package=rliger
  authors:
  - family-names: Welch
    given-names: Joshua
    email: welchjd@umich.edu
  - family-names: Wang
    given-names: Yichen
    email: wayichen@umich.edu
  - family-names: Gao
    given-names: Chao
    email: gchao@umich.edu
  - family-names: Liu
    given-names: Jialin
    email: alanliu@umich.edu
  - family-names: Sodicoff
    given-names: Joshua
    email: sodicoff@umich.edu
  - family-names: Kozareva
    given-names: Velina
  - family-names: Macosko
    given-names: Evan
  year: '2026'
  doi: 10.32614/CRAN.package.rliger
- type: software
  title: Routliers
  abstract: 'Routliers: Robust Outliers Detection'
  notes: Imports
  url: https://github.com/mdelacre/Routliers
  repository: https://CRAN.R-project.org/package=Routliers
  authors:
  - family-names: Delacre
    given-names: Marie
    email: marie.delacre@ulb.ac.be
  - family-names: Klein
    given-names: Olivier
    email: Klein.Olivier@ulb.ac.be
  year: '2026'
  doi: 10.32614/CRAN.package.Routliers
- type: software
  title: scDblFinder
  abstract: 'scDblFinder: scDblFinder'
  notes: Imports
  url: https://plger.github.io/scDblFinder/
  repository: https://bioconductor.org/
  authors:
  - family-names: Germain
    given-names: Pierre-Luc
    email: pierre-luc.germain@hest.ethz.ch
    orcid: https://orcid.org/0000-0003-3418-4218
  year: '2026'
  doi: 10.18129/B9.bioc.scDblFinder
- type: software
  title: Seurat
  abstract: 'Seurat: Tools for Single Cell Genomics'
  notes: Imports
  url: https://satijalab.org/seurat
  repository: https://CRAN.R-project.org/package=Seurat
  authors:
  - family-names: Satija
    given-names: Rahul
    email: seurat@nygenome.org
    orcid: https://orcid.org/0000-0001-9448-8833
  year: '2026'
  doi: 10.32614/CRAN.package.Seurat
- type: software
  title: SeuratObject
  abstract: 'SeuratObject: Data Structures for Single Cell Data'
  notes: Imports
  url: https://satijalab.github.io/seurat-object/
  repository: https://CRAN.R-project.org/package=SeuratObject
  authors:
  - family-names: Hoffman
    given-names: Paul
    email: hoff0792@alumni.umn.edu
    orcid: https://orcid.org/0000-0002-7693-8957
  - family-names: Satija
    given-names: Rahul
    email: seurat@nygenome.org
    orcid: https://orcid.org/0000-0001-9448-8833
  - family-names: Collins
    given-names: David
    email: dcollins@nygenome.org
    orcid: https://orcid.org/0000-0001-9243-7821
  - family-names: Hao
    given-names: Yuhan
    email: yhao@nygenome.org
    orcid: https://orcid.org/0000-0002-1810-0822
  - family-names: Hartman
    given-names: Austin
    email: ahartman@nygenome.org
    orcid: https://orcid.org/0000-0001-7278-1852
  - family-names: Molla
    given-names: Gesmira
    email: gmolla@nygenome.org
    orcid: https://orcid.org/0000-0002-8628-5056
  - family-names: Butler
    given-names: Andrew
    email: abutler@nygenome.org
    orcid: https://orcid.org/0000-0003-3608-0463
  - family-names: Stuart
    given-names: Tim
    email: tstuart@nygenome.org
    orcid: https://orcid.org/0000-0002-3044-0897
  year: '2026'
  doi: 10.32614/CRAN.package.SeuratObject
- type: software
  title: SeuratWrappers
  abstract: 'SeuratWrappers: Community-Provided Methods and Extensions for the Seurat
    Object'
  notes: Imports
  authors:
  - family-names: Butler
    given-names: Andrew
    email: abutler@nygenome.org
    orcid: https://orcid.org/0000-0003-3608-0463
  - family-names: Hoffman
    given-names: Paul
    email: nygcSatijalab@nygenome.org
    orcid: https://orcid.org/0000-0002-7693-8957
  - family-names: Satija
    given-names: Rahul
    email: rsatija@nygenome.org
    orcid: https://orcid.org/0000-0001-9448-8833
  - family-names: Stuart
    given-names: Tim
    email: tstuart@nygenome.org
    orcid: https://orcid.org/0000-0002-3044-0897
  year: '2026'
- type: software
  title: SingleR
  abstract: 'SingleR: Reference-Based Single-Cell RNA-Seq Annotation'
  notes: Imports
  url: https://github.com/SingleR-inc/SingleR
  repository: https://bioconductor.org/
  authors:
  - family-names: Aran
    given-names: Dvir
    email: dvir.aran@ucsf.edu
  year: '2026'
  doi: 10.18129/B9.bioc.SingleR
- type: software
  title: stats
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: 'R Foundation for Statistical Computing (ROR: <https://ror.org/05qewa988>)'
    address: Vienna, Austria
  year: '2026'
  doi: 10.32614/R.manuals
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: 'R Foundation for Statistical Computing (ROR: <https://ror.org/05qewa988>)'
    address: Vienna, Austria
  year: '2026'
  doi: 10.32614/R.manuals
- type: software
  title: cffr
  abstract: 'cffr: Generate Citation File Format (''cff'') Metadata for R Packages'
  notes: Suggests
  url: https://docs.ropensci.org/cffr/
  repository: https://CRAN.R-project.org/package=cffr
  authors:
  - family-names: Hernangómez
    given-names: Diego
    email: diego.hernangomezherrero@gmail.com
    orcid: https://orcid.org/0000-0001-8457-4658
  year: '2026'
  doi: 10.32614/CRAN.package.cffr
- type: software
  title: GSEABase
  abstract: 'GSEABase: Gene set enrichment data structures and methods'
  notes: Suggests
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
  - family-names: Falcon
    given-names: Seth
  - family-names: Gentleman
    given-names: Robert
  year: '2026'
  doi: 10.18129/B9.bioc.GSEABase
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2026'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: ontologyIndex
  abstract: 'ontologyIndex: Reading Ontologies into R'
  notes: Suggests
  repository: https://CRAN.R-project.org/package=ontologyIndex
  authors:
  - family-names: Greene
    given-names: Daniel
    email: dg333@cam.ac.uk
  year: '2026'
  doi: 10.32614/CRAN.package.ontologyIndex
- type: software
  title: R.utils
  abstract: 'R.utils: Various Programming Utilities'
  notes: Suggests
  url: https://henrikbengtsson.github.io/R.utils/
  repository: https://CRAN.R-project.org/package=R.utils
  authors:
  - family-names: Bengtsson
    given-names: Henrik
    email: henrikb@braju.com
  year: '2026'
  doi: 10.32614/CRAN.package.R.utils
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2026'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: roxygen2
  abstract: 'roxygen2: In-Line Documentation for R'
  notes: Suggests
  url: https://roxygen2.r-lib.org/
  repository: https://CRAN.R-project.org/package=roxygen2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Danenberg
    given-names: Peter
    email: pcd@roxygen.org
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  - family-names: Eugster
    given-names: Manuel
  year: '2026'
  doi: 10.32614/CRAN.package.roxygen2
- type: software
  title: SingleCellExperiment
  abstract: 'SingleCellExperiment: S4 Classes for Single Cell Data'
  notes: Suggests
  repository: https://bioconductor.org/
  authors:
  - family-names: Lun
    given-names: Aaron
    email: infinite.monkeys.with.keyboards@gmail.com
  - family-names: Risso
    given-names: Davide
    email: risso.davide@gmail.com
  year: '2026'
  doi: 10.18129/B9.bioc.SingleCellExperiment