Package: SingleCellMultiModal 1.19.1
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:
SingleCellMultiModal_1.19.1.tar.gz
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SingleCellMultiModal_1.19.1.tgz(r-4.4-any)SingleCellMultiModal_1.19.1.tgz(r-4.3-any)
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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
experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-package
Last updated 14 hours agofrom:0c4f175d8b. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 21 2024 |
R-4.5-win | OK | Nov 21 2024 |
R-4.5-linux | OK | Nov 21 2024 |
R-4.4-win | OK | Nov 21 2024 |
R-4.4-mac | OK | Nov 21 2024 |
R-4.3-win | OK | Nov 21 2024 |
R-4.3-mac | OK | Nov 21 2024 |
Exports:addCTLabelsCITEseqgetCellGroupsGTseqontomapremoveCachescmmCachescMultiomescNMTSCoPE2seqFISHsetCacheSingleCellMultiModal
Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyrExperimentHubfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglueHDF5ArrayhttrIRangesjsonliteKEGGRESTlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigplogrpngpurrrR6rappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLiteS4ArraysS4VectorsSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectoryamlzlibbioc
CITEseq Cord Blood
Rendered fromCITEseq.Rmd
usingknitr::rmarkdown
on Nov 21 2024.Last update: 2024-10-17
Started: 2020-10-20
ECCITEseq Peripheral Blood
Rendered fromECCITEseq.Rmd
usingknitr::rmarkdown
on Nov 21 2024.Last update: 2024-10-17
Started: 2021-01-07
G&T-seq Mouse Embryo (8-cell stage)
Rendered fromGTseq.Rmd
usingknitr::rmarkdown
on 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.Rmd
usingknitr::rmarkdown
on Nov 21 2024.Last update: 2024-10-17
Started: 2021-04-09
scNMT Mouse Gastrulation
Rendered fromscNMT.Rmd
usingknitr::rmarkdown
on Nov 21 2024.Last update: 2024-10-17
Started: 2020-04-01
SCoPE2: macrophage vs monocytes
Rendered fromSCoPE2.Rmd
usingknitr::rmarkdown
on Nov 21 2024.Last update: 2024-10-17
Started: 2021-01-19
seqFISH Mouse Visual Cortex
Rendered fromseqFISH.Rmd
usingknitr::rmarkdown
on Nov 21 2024.Last update: 2024-10-17
Started: 2020-09-23
SingleCellMultiModal Introduction
Rendered fromSingleCellMultiModal.Rmd
usingknitr::rmarkdown
on Nov 21 2024.Last update: 2024-10-17
Started: 2023-05-23
Readme and manuals
Help Manual
Help page | Topics |
---|---|
SingleCellMultiModal-package | SingleCellMultiModal-package |
addCTLabels | addCTLabels |
CITEseq | CITEseq |
getCellGroups | getCellGroups |
Parallel sequencing data of single-cell genomes and transcriptomes | GTseq |
Obtain a map of cell types for each dataset | ontomap |
Manage cache / download directories for study data | removeCache scmmCache setCache |
Single-cell Multiome ATAC + Gene Expression | scMultiome |
Single-cell Nucleosome, Methylation and Transcription sequencing | scNMT |
Single-cell RNA sequencing and proteomics | SCoPE2 |
Single-cell spatial + Gene Expression | seqFISH |
Combining Modalities into one MultiAssayExperiment | SingleCellMultiModal |