Parallel sequencing data of single-cell genomes and transcriptomes

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,
  ...
)

Source

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

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

Value

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

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

metadata

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

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.

Examples


GTseq()
#>    ah_id           mode file_size           rdataclass rdatadateadded
#> 1 EH5431        genomic      0 Mb     RaggedExperiment     2021-03-24
#> 2 EH5433 transcriptomic    2.3 Mb SingleCellExperiment     2021-03-24
#>   rdatadateremoved
#> 1             <NA>
#> 2             <NA>