scNMT | R Documentation |
scNMT assembles data on-the-fly from ExperimentHub
to
provide a MultiAssayExperiment container. The DataType
argument provides access to the mouse_gastrulation
dataset as obtained
from Argelaguet et al. (2019; DOI: 10.1038/s41586-019-1825-8).
Pre-processing code can be seen at
https://github.com/rargelaguet/scnmt_gastrulation. Protocol
information for this dataset is available at Clark et al. (2018). See
the vignette for the full citation.
scNMT(
DataType = "mouse_gastrulation",
modes = "*",
version = "1.0.0",
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. |
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 |
scNMT is a combination of RNA-seq (transcriptome) and an adaptation of Nucleosome Occupancy and Methylation sequencing (NOMe-seq, the methylome and chromatin accessibility) technologies. For more information, see Reik et al. (2018) DOI: 10.1038/s41467-018-03149-4
mouse_gastrulation:
this dataset provides cell quality control filters in the object
colData
starting from version 2.0.0.
Additionally, cell types annotations are provided through the lineage
colData
column.
rna - RNA-seq
acc_ - chromatin accessibility
met_ - DNA methylation
cgi - CpG islands
CTCF - footprints of CTCF binding
DHS - DNase Hypersensitive Sites
genebody - gene bodies
p300 - p300 binding sites
promoter - gene promoters
Special thanks to Al J Abadi for preparing the published data in time for the 2020 BIRS Workshop, see the link here: urlhttps://github.com/BIRSBiointegration/Hackathon/tree/master/scNMT-seq
A single cell multi-modal MultiAssayExperiment or
informative data.frame
when dry.run
is TRUE
Version '1.0.0' of the scNMT mouse_gastrulation dataset includes all of the above mentioned assay technologies with filtering of cells based on quality control metrics. Version '2.0.0' contains all of the cells without the QC filter and does not contain CTCF binding footprints or p300 binding sites.
The MultiAssayExperiment
metadata includes the original function call
that saves the function call and the data version requested.
http://ftp.ebi.ac.uk/pub/databases/scnmt_gastrulation/
Argelaguet et al. (2019)
SingleCellMultiModal-package
scNMT(DataType = "mouse_gastrulation", modes = "*",
version = "1.0.0", dry.run = TRUE)
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