CITATION.cff

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# 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 "SingleCellMultiModal" in publications use:'
type: software
license: Artistic-2.0
title: 'SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets'
version: 1.17.1
doi: 10.1371/journal.pcbi.1011324
abstract: SingleCellMultiModal is an ExperimentHub package that serves multiple datasets
  obtained from GEO and other sources and represents them as MultiAssayExperiment
  objects. We provide several multi-modal datasets including scNMT, 10X Multiome,
  seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide
  data for benchmarking and analysis.
authors:
- family-names: Ramos
  given-names: Marcel
  email: marcel.ramos@roswellpark.org
  orcid: https://orcid.org/0000-0002-3242-0582
- family-names: Argelaguet
  given-names: Ricard
  email: ricard@ebi.ac.uk
- family-names: Righelli
  given-names: Dario
  email: dario.righelli@gmail.com
- family-names: Eckenrode
  given-names: Kelly
  email: kelly.eckenrode@sph.cuny.edu
- family-names: Geistlinger
  given-names: Ludwig
  email: ludwig_geistlinger@hms.harvard.edu
- family-names: Waldron
  given-names: Levi
  email: lwaldron.research@gmail.com
preferred-citation:
  type: article
  title: Curated single cell multimodal landmark datasets for R/Bioconductor
  authors:
  - family-names: Eckenrode
    given-names: Kelly B
  - family-names: Righelli
    given-names: Dario
    email: dario.righelli@gmail.com
  - family-names: Ramos
    given-names: Marcel
    orcid: https://orcid.org/0000-0002-3242-0582
    email: marcel.ramos@roswellpark.org
  - family-names: Argelaguet
    given-names: Ricard
    email: ricard@ebi.ac.uk
  - family-names: Vanderaa
    given-names: Christophe
  - family-names: Geistlinger
    given-names: Ludwig
    orcid: https://orcid.org/0000-0002-2495-5464
    email: ludwig_geistlinger@hms.harvard.edu
  - family-names: Culhane
    given-names: Aedin C
  - family-names: Gatto
    given-names: Laurent
  - family-names: Carey
    given-names: Vincent J
    orcid: https://orcid.org/0000-0003-4046-0063
  - family-names: Morgan
    given-names: Martin
    orcid: https://orcid.org/0000-0002-5874-8148
  - family-names: Risso
    given-names: Davide
  - family-names: Waldron
    given-names: Levi
    orcid: https://orcid.org/0000-0003-2725-0694
    email: lwaldron.research@gmail.com
  journal: PLoS Comput. Biol.
  year: '2023'
  volume: '19'
  issue: '8'
  doi: 10.1371/journal.pcbi.1011324
repository: https://bioconductor.org/
repository-code: https://github.com/waldronlab/SingleCellMultiModal
url: https://github.com/waldronlab/SingleCellMultiModal
date-released: '2024-06-18'
contact:
- family-names: Ramos
  given-names: Marcel
  email: marcel.ramos@roswellpark.org
  orcid: https://orcid.org/0000-0002-3242-0582
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
    address: Vienna, Austria
  year: '2024'
  version: '>= 4.2.0'
- type: software
  title: MultiAssayExperiment
  abstract: 'MultiAssayExperiment: Software for the integration of multi-omics experiments
    in Bioconductor'
  notes: Depends
  url: http://waldronlab.io/MultiAssayExperiment/
  repository: https://bioconductor.org/
  authors:
  - family-names: Ramos
    given-names: Marcel
    email: marcel.ramos@roswellpark.org
    orcid: https://orcid.org/0000-0002-3242-0582
  - family-names: Morgan
    given-names: Martin
  - family-names: Carey
    given-names: Vincent J
  - family-names: Waldron
    given-names: Levi
    email: lwaldron.research@gmail.com
  year: '2024'
- type: software
  title: AnnotationHub
  abstract: 'AnnotationHub: Client to access AnnotationHub resources'
  notes: Imports
  url: https://github.com/Bioconductor/AnnotationHub
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
  - family-names: Shepherd
    given-names: Lori
  year: '2024'
- type: software
  title: BiocBaseUtils
  abstract: 'BiocBaseUtils: General utility functions for developing Bioconductor
    packages'
  notes: Imports
  url: https://www.github.com/Bioconductor/BiocBaseUtils
  repository: https://bioconductor.org/
  authors:
  - family-names: Ramos
    given-names: Marcel
    email: marcel.ramos@roswellpark.org
    orcid: https://orcid.org/0000-0002-3242-0582
  year: '2024'
- type: software
  title: BiocFileCache
  abstract: 'BiocFileCache: Manage Files Across Sessions'
  notes: Imports
  url: https://github.com/Bioconductor/BiocFileCache
  repository: https://bioconductor.org/
  authors:
  - family-names: Shepherd
    given-names: Lori
    email: lori.shepherd@roswellpark.org
  - family-names: Morgan
    given-names: Martin
    email: martin.morgan@roswellpark.org
  year: '2024'
- type: software
  title: ExperimentHub
  abstract: 'ExperimentHub: Client to access ExperimentHub resources'
  notes: Imports
  url: https://github.com/Bioconductor/ExperimentHub
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
  - family-names: Shepherd
    given-names: Lori
  year: '2024'
- type: software
  title: graphics
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- type: software
  title: HDF5Array
  abstract: 'HDF5Array: HDF5 backend for DelayedArray objects'
  notes: Imports
  url: https://bioconductor.org/packages/HDF5Array
  repository: https://bioconductor.org/
  authors:
  - family-names: Pagès
    given-names: Hervé
  year: '2024'
- type: software
  title: S4Vectors
  abstract: 'S4Vectors: Foundation of vector-like and list-like containers in Bioconductor'
  notes: Imports
  url: https://bioconductor.org/packages/S4Vectors
  repository: https://bioconductor.org/
  authors:
  - family-names: Pagès
    given-names: Hervé
    email: hpages.on.github@gmail.com
  - family-names: Lawrence
    given-names: Michael
  - family-names: Aboyoun
    given-names: Patrick
  year: '2024'
- type: software
  title: SingleCellExperiment
  abstract: 'SingleCellExperiment: S4 Classes for Single Cell Data'
  notes: Imports
  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: '2024'
- type: software
  title: SpatialExperiment
  abstract: 'SpatialExperiment: S4 Class for Spatially Resolved -omics Data'
  notes: Imports
  url: https://github.com/drighelli/SpatialExperiment
  repository: https://bioconductor.org/
  authors:
  - family-names: Righelli
    given-names: Dario
    email: dario.righelli@gmail.com
  - family-names: Risso
    given-names: Davide
    email: risso.davide@gmail.com
  - family-names: Crowell
    given-names: Helena L.
    email: helena.crowell@uzh.ch
  - family-names: Weber
    given-names: Lukas M.
    email: lukas.weber.edu@gmail.com
  year: '2024'
- type: software
  title: SummarizedExperiment
  abstract: 'SummarizedExperiment: SummarizedExperiment container'
  notes: Imports
  url: https://bioconductor.org/packages/SummarizedExperiment
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
  - family-names: Obenchain
    given-names: Valerie
  - family-names: Hester
    given-names: Jim
  - family-names: Pagès
    given-names: Hervé
    email: hpages.on.github@gmail.com
  year: '2024'
- type: software
  title: Matrix
  abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
  notes: Imports
  url: https://R-forge.R-project.org/tracker/?atid=294&group_id=61
  repository: https://CRAN.R-project.org/package=Matrix
  authors:
  - family-names: Bates
    given-names: Douglas
    orcid: https://orcid.org/0000-0001-8316-9503
  - family-names: Maechler
    given-names: Martin
    email: mmaechler+Matrix@gmail.com
    orcid: https://orcid.org/0000-0002-8685-9910
  - family-names: Jagan
    given-names: Mikael
    orcid: https://orcid.org/0000-0002-3542-2938
  year: '2024'
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- 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
    address: Vienna, Austria
  year: '2024'
- type: software
  title: BiocStyle
  abstract: 'BiocStyle: Standard styles for vignettes and other Bioconductor documents'
  notes: Suggests
  url: https://github.com/Bioconductor/BiocStyle
  repository: https://bioconductor.org/
  authors:
  - family-names: Oleś
    given-names: Andrzej
    orcid: https://orcid.org/0000-0003-0285-2787
  year: '2024'
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Suggests
  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: '2024'
- 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: '2024'
- type: software
  title: RaggedExperiment
  abstract: 'RaggedExperiment: Representation of Sparse Experiments and Assays Across
    Samples'
  notes: Suggests
  url: https://github.com/Bioconductor/RaggedExperiment
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
    email: martin.morgan@roswellpark.org
  - family-names: Ramos
    given-names: Marcel
    email: marcel.ramos@roswellpark.org
    orcid: https://orcid.org/0000-0002-3242-0582
  year: '2024'
- 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: '2024'
- type: software
  title: scater
  abstract: 'scater: Single-Cell Analysis Toolkit for Gene Expression Data in R'
  notes: Suggests
  url: https://support.bioconductor.org/
  repository: https://bioconductor.org/
  authors:
  - family-names: McCarthy
    given-names: Davis
    email: davis@ebi.ac.uk
  - family-names: Campbell
    given-names: Kieran
    email: kieran.campbell@sjc.ox.ac.uk
  - family-names: Lun
    given-names: Aaron
    email: infinite.monkeys.with.keyboards@gmail.com
  - family-names: Wills
    given-names: Quin
    email: qilin@quinwills.net
  year: '2024'
- type: software
  title: UpSetR
  abstract: 'UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing
    Intersecting Sets'
  notes: Suggests
  url: http://github.com/hms-dbmi/UpSetR
  repository: https://CRAN.R-project.org/package=UpSetR
  authors:
  - family-names: Gehlenborg
    given-names: Nils
    email: nils@hms.harvard.edu
  year: '2024'
- type: software
  title: uwot
  abstract: 'uwot: The Uniform Manifold Approximation and Projection (UMAP) Method
    for Dimensionality Reduction'
  notes: Suggests
  url: https://jlmelville.github.io/uwot/
  repository: https://CRAN.R-project.org/package=uwot
  authors:
  - family-names: Melville
    given-names: James
    email: jlmelville@gmail.com
  year: '2024'