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

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SingleCellMultiModal")

Load

library(SingleCellMultiModal)
library(MultiAssayExperiment)

G&T-seq: parallel sequencing data of single-cell genomes and transcriptomes

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 @Macaulay2015.

Downloading datasets

The user can see the available dataset by using the default options

GTseq("mouse_embryo_8_cell", mode = "*", dry.run = TRUE)

Or by simply running:

GTseq()

Obtaining the data

To obtain the actual datasets:

gts <- GTseq(dry.run = FALSE)
gts

Exploring the data structure

Check available metadata for each of the 112 mouse embryo cells assayed by G&T-seq:

colData(gts)

Take a peek at the sampleMap:

sampleMap(gts)

Copy numbers

To access the integer copy numbers as detected from scDNA-seq:

head(assay(gts, "genomic"))[, 1:4]

RNA-seq

To access raw read counts as quantified from scRNA-seq:

head(assay(gts, "transcriptomic"))[, 1:4]

For protocol information, see @Macaulay2016.

sessionInfo

sessionInfo()

References

waldronlab/SingleCellMultiModal documentation built on May 1, 2024, 5:29 a.m.