Package: SingleCellMultiModal 1.17.3

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]

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

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

Peer review:

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

On CRAN:

experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-package

13 exports 17 stars 2.14 score 81 dependencies 53 scripts

Last updated 3 months agofrom:1ac9a1f701. Checks:OK: 1 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 16 2024
R-4.5-winNOTESep 16 2024
R-4.5-linuxNOTESep 16 2024
R-4.4-winNOTESep 16 2024
R-4.4-macNOTESep 16 2024
R-4.3-winNOTEAug 17 2024
R-4.3-macNOTEAug 17 2024

Exports:addCTLabelsCITEseqgetCellGroupsGTseqontomapremoveCachescmmCachescMultiomescNMTSCoPE2seqFISHsetCacheSingleCellMultiModal

Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyrExperimentHubfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglueHDF5ArrayhttrIRangesjsonliteKEGGRESTlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigplogrpngpurrrR6rappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLiteS4ArraysS4VectorsSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectoryamlzlibbioc

CITEseq Cord Blood

Dario Righelli

Rendered fromCITEseq.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2023-07-11
Started: 2020-10-20

ECCITEseq Peripheral Blood

Dario Righelli

Rendered fromECCITEseq.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2023-07-11
Started: 2021-01-07

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

Rendered fromGTseq.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2021-03-25
Started: 2021-03-25

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

Rendered fromscMultiome.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2021-04-09
Started: 2021-04-09

scNMT Mouse Gastrulation

Rendered fromscNMT.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2021-10-15
Started: 2020-04-01

SCoPE2: macrophage vs monocytes

Rendered fromSCoPE2.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2023-05-28
Started: 2021-01-19

seqFISH Mouse Visual Cortex

Dario Righelli

Rendered fromseqFISH.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2021-10-15
Started: 2020-09-23

SingleCellMultiModal Introduction

Rendered fromSingleCellMultiModal.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2024-06-18
Started: 2023-05-23