scMultiome | R Documentation |
10x Genomics Multiome technology enables simultaneous profiling of the transcriptome (using 3’ gene expression) and epigenome (using ATAC-seq) from single cells to deepen our understanding of how genes are expressed and regulated across different cell types. Data prepared by Ricard Argelaguet.
scMultiome(
DataType = "pbmc_10x",
modes = "*",
version = "1.0.0",
format = c("MTX", "HDF5"),
dry.run = TRUE,
verbose = TRUE,
...
)
DataType |
character(1) Indicates study that produces this type of data (default: 'mouse_gastrulation') |
modes |
character() A wildcard / glob pattern of modes, such as
|
version |
character(1) Either version '1.0.0' or '2.0.0' depending on data version required (default '1.0.0'). See version section. |
format |
Either MTX or HDF5 data format (default MTX) |
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 |
Users are able to choose from either an MTX
or HDF5
file format
as the internal data representation. The MTX
(Matrix Market)
format allows users to load a sparse dgCMatrix
representation.
Choosing HDF5
gives users a sparse HDF5Array
class object.
pbmc_10x: 10K Peripheral Blood Mononuclear Cells provided by
10x Genomics website
Cell quality control filters are available in the object colData
together with the celltype
annotation labels.
A 10X PBMC MultiAssayExperiment
object
scMultiome(DataType = "pbmc_10x", modes = "*", dry.run = TRUE)
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