Package: SingleCellMultiModal 1.25.3

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
SingleCellMultiModal_1.25.3.zip(r-4.7)SingleCellMultiModal_1.25.3.zip(r-4.6)SingleCellMultiModal_1.25.3.zip(r-4.5)
SingleCellMultiModal_1.25.3.tgz(r-4.6-any)SingleCellMultiModal_1.25.3.tgz(r-4.5-any)
SingleCellMultiModal_1.25.3.tar.gz(r-4.7-any)SingleCellMultiModal_1.25.3.tar.gz(r-4.6-any)
SingleCellMultiModal_1.25.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SingleCellMultiModal/json (API)
NEWS

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

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

On CRAN:

Conda:

experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073

7.48 score 18 stars 88 scripts 13 exports 80 dependencies

Last updated from:cdbd97d961. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK358
source / vignettesOK500
linux-release-x86_64OK389
macos-release-arm64OK260
macos-oldrel-arm64OK247
windows-develOK324
windows-releaseOK289
windows-oldrelOK367
wasm-releaseOK180

Exports:addCTLabelsCITEseqgetCellGroupsGTseqontomapremoveCachescmmCachescMultiomescNMTSCoPE2seqFISHsetCacheSingleCellMultiModal

Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydir.expirydplyrExperimentHubfastmapfilelockgenericsGenomicRangesglueh5mreadHDF5Arrayhttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigpngpurrrR6rappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVectoryaml

CITEseq Cord Blood

Dario Righelli

Rendered fromCITEseq.Rmdusingknitr::rmarkdownon May 29 2026.

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

ECCITEseq Peripheral Blood

Dario Righelli

Rendered fromECCITEseq.Rmdusingknitr::rmarkdownon May 29 2026.

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

G&T-seq Mouse Embryo (8-cell stage)

Ludwig Geistlinger

Rendered fromGTseq.Rmdusingknitr::rmarkdownon May 29 2026.

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

PBMCs profiled with the Chromium Single Cell Multiome ATAC + Gene Expression from 10x

Marcel Ramos Pérez, Al J Abadi, Ricard Argelaguet, Levi Waldron

Rendered fromscMultiome.Rmdusingknitr::rmarkdownon May 29 2026.

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

scNMT Mouse Gastrulation

Marcel Ramos Pérez

Rendered fromscNMT.Rmdusingknitr::rmarkdownon May 29 2026.

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

SCoPE2: macrophage vs monocytes

Christophe Vanderaa

Rendered fromSCoPE2.Rmdusingknitr::rmarkdownon May 29 2026.

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

seqFISH Mouse Visual Cortex

Dario Righelli

Rendered fromseqFISH.Rmdusingknitr::rmarkdownon May 29 2026.

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

SingleCellMultiModal Introduction

Rendered fromSingleCellMultiModal.Rmdusingknitr::rmarkdownon May 29 2026.

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