GTseq: Parallel sequencing data of single-cell genomes and...

In waldronlab/SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets

Parallel sequencing data of single-cell genomes and transcriptomes

Description

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.

Usage

GTseq(
  DataType = "mouse_embryo_8_cell",
  modes = "*",
  version = "1.0.0",
  dry.run = TRUE,
  verbose = TRUE,
  ...
)

Arguments

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 "*omic". A wildcard of "*" will return all modes including copy numbers ("genomic") and RNA-seq read counts ("transcriptomic"), which is the default.
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 constructor

Details

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

Value

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

metadata

The MultiAssayExperiment metadata includes the original function call that saves the function call and the data version requested.

Source

https://www.ebi.ac.uk/ena/browser/view/PRJEB9051

References

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.

See Also

SingleCellMultiModal-package

Examples

GTseq()

waldronlab/SingleCellMultiModal documentation built on Nov. 23, 2024, 3:46 p.m.