SCoPE2 | R Documentation |
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.
SCoPE2(
DataType = "macrophage_differentiation",
modes = "*",
version = "1.0.0",
dry.run = TRUE,
verbose = TRUE,
...
)
DataType |
character(1) Indicates study that produces this type of data (default: 'macrophage_differentiation') |
modes |
character() A wildcard / glob pattern of modes, such as
|
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 |
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
A single cell multi-modal MultiAssayExperiment or
informative data.frame
when dry.run
is TRUE
All files are linked from the slavovlab website https://scope2.slavovlab.net/docs/data
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.
SingleCellMultiModal-package
SCoPE2(DataType = "macrophage_differentiation",
modes = "*",
version = "1.0.0",
dry.run = TRUE)
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