GTseq | R Documentation |
GTseq assembles data on-the-fly from ExperimentHub
to
provide a MultiAssayExperiment container. The DataType
argument provides access to the mouse_embryo_8_cell
dataset as obtained
from Macaulay et al. (2015). Protocol information for this dataset is
available from Macaulay et al. (2016). See references.
GTseq(
DataType = "mouse_embryo_8_cell",
modes = "*",
version = "1.0.0",
dry.run = TRUE,
verbose = TRUE,
...
)
DataType |
character(1) Indicates study that produces this type of data (default: 'mouse_embryo_8_cell') |
modes |
character() A wildcard / glob pattern of modes, such as
|
version |
character(1). Currently, only version '1.0.0'. |
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 |
G&T-seq is a combination of Picoplex amplified gDNA sequencing (genome) and SMARTSeq2 amplified cDNA sequencing (transcriptome) of the same cell. For more information, see Macaulay et al. (2015).
mouse_embryo_8_cell: this dataset was filtered for bad cells as specified in Macaulay et al. (2015).
genomic - integer copy numbers as detected from scDNA-seq
transcriptomic - raw read counts as quantified from scRNA-seq
A single cell multi-modal MultiAssayExperiment or
informative data.frame
when dry.run
is TRUE
The MultiAssayExperiment
metadata includes the original function call
that saves the function call and the data version requested.
https://www.ebi.ac.uk/ena/browser/view/PRJEB9051
Macaulay et al. (2015) G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat Methods, 12:519–22.
Macaulay et al. (2016) Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq. Nat Protoc, 11:2081–103.
SingleCellMultiModal-package
GTseq()
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