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Single-cell RNA sequencing and proteomics

Source: R/SCoPE2.R
SCoPE2.Rd

SCoPE2 assembles data on-the-fly from ExperimentHub to provide a MultiAssayExperiment container. The DataType argument provides access to the SCoPE2 dataset as provided by Specht et al. (2020; DOI: http://dx.doi.org/10.1101/665307). The article provides more information about the data acquisition and pre-processing.

Usage

SCoPE2(
  DataType = "macrophage_differentiation",
  modes = "*",
  version = "1.0.0",
  dry.run = TRUE,
  verbose = TRUE,
  ...
)

Source

All files are linked from the slavovlab website https://scope2.slavovlab.net/docs/data

Arguments

DataType

character(1) Indicates study that produces this type of data (default: 'macrophage_differentiation')

modes

character() A wildcard / glob pattern of modes, such as "rna". A wildcard of "*" will return all modes, that are transcriptome ("rna") or proteome ("protein") which is the default.

version

character(1), currently only version '1.0.0' is available

dry.run

logical(1) Whether to return the dataset names before actual download (default TRUE)

verbose

logical(1) Whether to show the dataset currently being (down)loaded (default TRUE)

...

Additional arguments passed on to the ExperimentHub-class constructor

Value

A single cell multi-modal MultiAssayExperiment or informative data.frame when dry.run is TRUE

Details

The SCoPE2 study combines scRNA-seq (transcriptome) and single-cell proteomics.

  • macrophage_differentiation: the cells are monocytes that undergo macrophage differentiation. No annotation is available for the transcriptome data, but batch and cell type annotations are available for the proteomics data in the celltype colData column. The transcriptomics and proteomics data were not measured from the same cells but from a distinct set of cell cultures. This dataset provides already filtered bad quality cells.

    • scRNAseq1 - single-cell transcriptome (batch 1)

    • scRNAseq2 - single-cell transcriptome (batch 2)

    • scp - single-cell proteomics

References

Specht, Harrison, Edward Emmott, Aleksandra A. Petelski, R. Gray Huffman, David H. Perlman, Marco Serra, Peter Kharchenko, Antonius Koller, and Nikolai Slavov. 2020. “Single-Cell Proteomic and Transcriptomic Analysis of Macrophage Heterogeneity.” bioRxiv. https://doi.org/10.1101/665307.

See also

SingleCellMultiModal-package

Examples


SCoPE2(DataType = "macrophage_differentiation",
       modes = "*",
       version = "1.0.0",
       dry.run = TRUE)
#>    ah_id       mode file_size           rdataclass rdatadateadded
#> 1 EH4694    protein   33.1 Mb SingleCellExperiment     2020-09-24
#> 2 EH4695 rna_assays   68.7 Mb           HDF5Matrix     2020-09-24
#> 3 EH4696     rna_se    0.2 Mb SingleCellExperiment     2020-09-24
#>   rdatadateremoved
#> 1             <NA>
#> 2             <NA>
#> 3             <NA>