WeberDivechaLCdata

This package contains data from our paper on the single-nucleus and spatially-resolved landscape of gene expression in the human locus coeruleus (LC).

The package is available from Bioconductor (WeberDivechaLCdata).

Datasets are stored in R/Bioconductor formats (SingleCellExperiment and SpatialExperiment).

The paper is available from eLife.

Installation

The data package is available from Bioconductor (WeberDivechaLCdata) and can be installed as follows:

install.packages("BiocManager")
BiocManager::install("WeberDivechaLCdata")

Contents

The package contains two objects:

• 1x SpatialExperiment formatted R object containing the SRT data
• 1x SingleCellExperiment formatted R object containing the snRNA-seq data

Loading the data

The R/Bioconductor data objects can be loaded as follows:

library(SpatialExperiment)
library(SingleCellExperiment)
library(WeberDivechaLCdata)

# Load objects using dataset names
spe <- WeberDivechaLCdata_Visium()
sce <- WeberDivechaLCdata_singleNucleus()

# Show objects
spe
sce

More details including alternative ways to load the data and details on the data structure are provided in the package vignette, which can be found on the Bioconductor package page (WeberDivechaLCdata) or directly here.

Citation

• Weber L.M.*, Divecha H.R.*, Tran M.N., Kwon S.H., Spangler A., Montgomery K.D., Tippani M., Bharadwaj R., Kleinman J.E., Page S.C., Hyde T.M., Collado-Torres L., Maynard K.R., Martinowich K.*, and Hicks S.C.* (2023). The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. eLife, 12:RP84628.