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'))

Peer review:

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

On CRAN:

experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-package

7.27 score 17 stars 57 scripts 13 exports 81 dependencies

Last updated 14 hours agofrom:0c4f175d8b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winOKNov 21 2024
R-4.5-linuxOKNov 21 2024
R-4.4-winOKNov 21 2024
R-4.4-macOKNov 21 2024
R-4.3-winOKNov 21 2024
R-4.3-macOKNov 21 2024

Exports:addCTLabelsCITEseqgetCellGroupsGTseqontomapremoveCachescmmCachescMultiomescNMTSCoPE2seqFISHsetCacheSingleCellMultiModal

Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyrExperimentHubfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglueHDF5ArrayhttrIRangesjsonliteKEGGRESTlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigplogrpngpurrrR6rappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLiteS4ArraysS4VectorsSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectoryamlzlibbioc

CITEseq Cord Blood

Rendered fromCITEseq.Rmdusingknitr::rmarkdownon Nov 21 2024.

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

ECCITEseq Peripheral Blood

Rendered fromECCITEseq.Rmdusingknitr::rmarkdownon Nov 21 2024.

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

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

Rendered fromGTseq.Rmdusingknitr::rmarkdownon Nov 21 2024.

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 Nov 21 2024.

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

scNMT Mouse Gastrulation

Rendered fromscNMT.Rmdusingknitr::rmarkdownon Nov 21 2024.

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

SCoPE2: macrophage vs monocytes

Rendered fromSCoPE2.Rmdusingknitr::rmarkdownon Nov 21 2024.

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

seqFISH Mouse Visual Cortex

Rendered fromseqFISH.Rmdusingknitr::rmarkdownon Nov 21 2024.

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

SingleCellMultiModal Introduction

Rendered fromSingleCellMultiModal.Rmdusingknitr::rmarkdownon Nov 21 2024.

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