Package: SingleCellMultiModal 1.25.3

Marcel Ramos

SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets

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. To cite, use the 'citation' function and see <https://doi.org/10.1371/journal.pcbi.1011324>.

Authors:Marcel Ramos [aut, cre], Ricard Argelaguet [aut], Al Abadi [ctb], Dario Righelli [aut], Christophe Vanderaa [ctb], Kelly Eckenrode [aut], Ludwig Geistlinger [aut], Levi Waldron [aut], NCI [fnd]

SingleCellMultiModal_1.25.3.tar.gz
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SingleCellMultiModal_1.25.3.tgz(r-4.6-any)SingleCellMultiModal_1.25.3.tgz(r-4.5-any)
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SingleCellMultiModal_1.25.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SingleCellMultiModal/json (API)

# Install 'SingleCellMultiModal' in R:
install.packages('SingleCellMultiModal', repos = c('https://waldronlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/waldronlab/singlecellmultimodal/issues

On CRAN:

Conda:

experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073

7.47 score 18 stars 102 scripts 13 exports 80 dependencies

Last updated from:cdbd97d961. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK374
source / vignettesOK480
linux-release-x86_64OK396
macos-release-arm64OK247
macos-oldrel-arm64OK189
windows-develOK295
windows-releaseOK283
windows-oldrelOK288
wasm-releaseOK174

Exports:addCTLabelsCITEseqgetCellGroupsGTseqontomapremoveCachescmmCachescMultiomescNMTSCoPE2seqFISHsetCacheSingleCellMultiModal

Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydir.expirydplyrExperimentHubfastmapfilelockgenericsGenomicRangesglueh5mreadHDF5Arrayhttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigpngpurrrR6rappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVectoryaml

G&T-seq Mouse Embryo (8-cell stage)
Installation | Load | G&T-seq: parallel sequencing data of single-cell genomes and transcriptomes | Downloading datasets | Obtaining the data | Exploring the data structure | Copy numbers | RNA-seq | sessionInfo | References
Rendered fromGTseq.Rmdusingknitr::rmarkdown

Last update: 2025-06-12
Started: 2021-03-25

PBMCs profiled with the Chromium Single Cell Multiome ATAC + Gene Expression from 10x
Installation | Load | Description | Downloading datasets | Exploring the data structure | Cell metadata | RNA expression | Chromatin Accessibility | Suggested software for the downstream analysis | sessionInfo
Rendered fromscMultiome.Rmdusingknitr::rmarkdown

Last update: 2025-06-12
Started: 2021-04-09

scNMT Mouse Gastrulation
Installation | Load packages | scNMT: single-cell nucleosome, methylation and transcription sequencing | Dataset lookup | Data versions | Downloading the data | Checking the cell metadata | Exploring the data structure | Chromatin Accessibility (acc_*) | DNA Methylation (met_*) | sessionInfo | References
Rendered fromscNMT.Rmdusingknitr::rmarkdown

Last update: 2025-06-12
Started: 2020-04-01

SCoPE2: macrophage vs monocytes
Installation | Load packages | SCoPE2 | Downloading data sets | Available projects | Retrieving data | The macrophage differentiation project | Data versions | Cell annotation | Transcriptomic data | Proteomic data | sessionInfo | References
Rendered fromSCoPE2.Rmdusingknitr::rmarkdown

Last update: 2025-06-12
Started: 2021-01-19

ECCITEseq Peripheral Blood
Installation | Load libraries | ECCITE-seq dataset | Downloading datasets | Exploring the data structure | scRNA-seq data | scADT data | CTCL/CTRL conditions | sgRNAs CRISPR pertubation data | SingleCellExperiment object conversion | Session Info | Additional References | References
Rendered fromECCITEseq.Rmdusingknitr::rmarkdown

Last update: 2024-10-17
Started: 2021-01-07

CITEseq Cord Blood
Installation | Load libraries | CITE-seq dataset | Downloading datasets | Exploring the data structure | scRNA-seq data | scADT data | SingleCellExperiment object conversion | Session Info | References
Rendered fromCITEseq.Rmdusingknitr::rmarkdown

Last update: 2024-10-17
Started: 2020-10-20

seqFISH Mouse Visual Cortex
Installation | Load packages | seq-FISH dataset | Downloading datasets | Exploring the data structure | Visualize matching cell identifiers across assays | scRNA-seq data | seq-FISH data | Other data version | Data version 1.0.0 | Session Info
Rendered fromseqFISH.Rmdusingknitr::rmarkdown

Last update: 2024-10-17
Started: 2020-09-23

SingleCellMultiModal Introduction
SingleCellMultiModal | Overview | Installation | Loading packages | Citing SingleCellMultiModal | Representation | Contributions | Further resources | References
Rendered fromSingleCellMultiModal.Rmdusingknitr::rmarkdown

Last update: 2024-10-17
Started: 2023-05-23