singlecellmultimodal

This is a read-only mirror of the git repos at https://bioconductor.org

https://github.com/bioc/singlecellmultimodal

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Repository

This is a read-only mirror of the git repos at https://bioconductor.org

Basic Info

Host: GitHub
Owner: bioc
Language: R
Default Branch: devel
Size: 740 KB

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Created almost 3 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog Citation

SingleCellMultiModal

Overview

SingleCellMultiModal is an R package that provides a convenient and user-friendly representation of multi-modal data using MultiAssayExperiment. This package introduces a suite of single-cell multimodal landmark datasets for benchmarking and testing multimodal analysis methods via the ExperimentHub Bioconductor package. The scope of this package is to provide efficient access to a selection of curated, pre-integrated, publicly available landmark datasets for methods development and benchmarking.

Installation

``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("SingleCellMultiModal") ```

Loading packages

r library(SingleCellMultiModal) library(MultiAssayExperiment)

Citing SingleCellMultiModal

Your citations are crucial in keeping our software free and open source. To cite our package see the citation (Eckenrode et al. (2023)) in the Reference section. You may also browse to the publication at PLoS Computational Biology.

Representation

Users can obtain integrative representations of multiple modalities as a MultiAssayExperiment, a common core Bioconductor data structure relied on by dozens of multimodal data analysis packages. MultiAssayExperiment harmonizes data management of multiple experimental assays performed on an overlapping set of specimens. Although originally developed for patient data from multi-omics cancer studies, the MultiAssayExperiment framework naturally applies also to single cells. A schematic of the data structure can be seen below. In this context, “patients” are replaced by “cells”. We use MultiAssayExperiment because it provides a familiar user experience by extending SummarizedExperiment concepts and providing open ended compatibility with standard data classes present in Bioconductor such as the SingleCellExperiment.

Contributions

Want to contribute to the SingleCellMultiModal package? We welcome contributions from the community. Please refer to our Contributing Guidelines for more details.

Further resources

For more information on the MultiAssayExperiment data structure, please refer to Ramos et al. (2017) as well as the MultiAssayExperiment vignette.

References

Eckenrode, Kelly B, Dario Righelli, Marcel Ramos, Ricard Argelaguet, Christophe Vanderaa, Ludwig Geistlinger, Aedin C Culhane, et al. 2023. “Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor.” *PLoS Comput. Biol.* 19 (8): e1011324.

Ramos, Marcel, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, et al. 2017. “Software for the Integration of Multiomics Experiments in Bioconductor.” *Cancer Res.* 77 (21): e39–42.

Owner

Name: bioc
Login: bioc
Kind: organization

Repositories: 1
Profile: https://github.com/bioc

Citation (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 "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:
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  notes: Depends
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  authors:
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    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
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  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
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    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
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  url: https://github.com/Bioconductor/BiocFileCache
  repository: https://bioconductor.org/
  authors:
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    email: lori.shepherd@roswellpark.org
  - family-names: Morgan
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  year: '2024'
- type: software
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  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:
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- type: software
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  notes: Imports
  url: https://bioconductor.org/packages/HDF5Array
  repository: https://bioconductor.org/
  authors:
  - family-names: Pagès
    given-names: Hervé
  year: '2024'
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  notes: Imports
  url: https://bioconductor.org/packages/S4Vectors
  repository: https://bioconductor.org/
  authors:
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    given-names: Hervé
    email: hpages.on.github@gmail.com
  - family-names: Lawrence
    given-names: Michael
  - family-names: Aboyoun
    given-names: Patrick
  year: '2024'
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  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
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  year: '2024'
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  abstract: 'SpatialExperiment: S4 Class for Spatially Resolved -omics Data'
  notes: Imports
  url: https://github.com/drighelli/SpatialExperiment
  repository: https://bioconductor.org/
  authors:
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    given-names: Dario
    email: dario.righelli@gmail.com
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  - family-names: Crowell
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  year: '2024'
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  notes: Imports
  url: https://bioconductor.org/packages/SummarizedExperiment
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
  - family-names: Obenchain
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  - family-names: Hester
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  - family-names: Pagès
    given-names: Hervé
    email: hpages.on.github@gmail.com
  year: '2024'
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  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:
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    orcid: https://orcid.org/0000-0001-8316-9503
  - family-names: Maechler
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    orcid: https://orcid.org/0000-0002-8685-9910
  - family-names: Jagan
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    orcid: https://orcid.org/0000-0002-3542-2938
  year: '2024'
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  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
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  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:
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
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    orcid: https://orcid.org/0000-0003-0285-2787
  year: '2024'
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  notes: Suggests
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  repository: https://CRAN.R-project.org/package=ggplot2
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    given-names: Hadley
    email: hadley@posit.co
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    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
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    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
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    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2024'
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  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'
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  abstract: 'RaggedExperiment: Representation of Sparse Experiments and Assays Across
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  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
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    orcid: https://orcid.org/0000-0002-3242-0582
  year: '2024'
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  notes: Suggests
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  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
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    email: rich@posit.co
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  year: '2024'
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  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
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  - family-names: Lun
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    email: infinite.monkeys.with.keyboards@gmail.com
  - family-names: Wills
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  year: '2024'
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  notes: Suggests
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  repository: https://CRAN.R-project.org/package=UpSetR
  authors:
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  repository: https://CRAN.R-project.org/package=uwot
  authors:
  - family-names: Melville
    given-names: James
    email: jlmelville@gmail.com
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Dependencies

DESCRIPTION cran

MultiAssayExperiment * depends
R >= 4.2.0 depends
AnnotationHub * imports
BiocBaseUtils * imports
BiocFileCache * imports
ExperimentHub * imports
HDF5Array * imports
Matrix * imports
S4Vectors * imports
SingleCellExperiment * imports
SpatialExperiment * imports
SummarizedExperiment * imports
graphics * imports
methods * imports
utils * imports
BiocStyle * suggests
RaggedExperiment * suggests
UpSetR * suggests
ggplot2 * suggests
knitr * suggests
rmarkdown * suggests
scater * suggests
scran * suggests
uwot * suggests

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