Package: SingleCellMultiModal 1.19.1

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]

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SingleCellMultiModal.pdf |SingleCellMultiModal.html✨
SingleCellMultiModal/json (API)
NEWS

# 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:

experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073

7.29 score 17 stars 60 scripts 13 exports 81 dependencies

Last updated 3 months agofrom:0c4f175d8b. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 19 2025
R-4.5-winOKJan 20 2025
R-4.5-macOKFeb 19 2025
R-4.5-linuxOKFeb 19 2025
R-4.4-winOKJan 20 2025
R-4.4-macOKFeb 19 2025
R-4.3-winOKDec 21 2024
R-4.3-macOKDec 21 2024

Exports:addCTLabelsCITEseqgetCellGroupsGTseqontomapremoveCachescmmCachescMultiomescNMTSCoPE2seqFISHsetCacheSingleCellMultiModal

Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyrExperimentHubfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglueh5mreadHDF5ArrayhttrIRangesjsonliteKEGGRESTlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigplogrpngpurrrR6rappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLiteS4ArraysS4VectorsSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectoryaml

CITEseq Cord Blood

Dario Righelli

Rendered fromCITEseq.Rmdusingknitr::rmarkdownon Feb 19 2025.

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

ECCITEseq Peripheral Blood

Dario Righelli

Rendered fromECCITEseq.Rmdusingknitr::rmarkdownon Feb 19 2025.

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

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

Rendered fromGTseq.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2024-10-17
Started: 2021-03-25

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

Rendered fromscMultiome.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2024-10-17
Started: 2021-04-09

scNMT Mouse Gastrulation

Rendered fromscNMT.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2024-10-17
Started: 2020-04-01

SCoPE2: macrophage vs monocytes

Rendered fromSCoPE2.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2024-10-17
Started: 2021-01-19

seqFISH Mouse Visual Cortex

Dario Righelli

Rendered fromseqFISH.Rmdusingknitr::rmarkdownon Feb 19 2025.

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

SingleCellMultiModal Introduction

Rendered fromSingleCellMultiModal.Rmdusingknitr::rmarkdownon Feb 19 2025.

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