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https://github.com/lmweber/weberdivechalcdata
Data package containing single-nucleus and spatially-resolved gene expression data from the human locus coeruleus (LC)
https://github.com/lmweber/weberdivechalcdata
Last synced: 2 days ago
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Data package containing single-nucleus and spatially-resolved gene expression data from the human locus coeruleus (LC)
- Host: GitHub
- URL: https://github.com/lmweber/weberdivechalcdata
- Owner: lmweber
- License: mit
- Created: 2022-10-04T18:27:46.000Z (about 2 years ago)
- Default Branch: devel
- Last Pushed: 2024-03-17T19:09:43.000Z (8 months ago)
- Last Synced: 2024-10-11T22:26:36.030Z (28 days ago)
- Language: R
- Homepage:
- Size: 37.1 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# WeberDivechaLCdata
[](https://github.com/lmweber/WeberDivechaLCdata/actions)
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](https://bioconductor.org/packages/WeberDivechaLCdata)).
Datasets are stored in R/Bioconductor formats ([SingleCellExperiment](https://bioconductor.org/packages/SingleCellExperiment) and [SpatialExperiment](https://bioconductor.org/packages/SpatialExperiment)).
The paper is available from [eLife](https://elifesciences.org/articles/84628).
## Installation
The data package is available from Bioconductor ([WeberDivechaLCdata](https://bioconductor.org/packages/WeberDivechaLCdata)) and can be installed as follows:
```
install.packages("BiocManager")
BiocManager::install("WeberDivechaLCdata")
```
## Contents
The package contains two objects:
- 1x [SpatialExperiment](https://bioconductor.org/packages/SpatialExperiment) formatted R object containing the SRT data
- 1x [SingleCellExperiment](https://bioconductor.org/packages/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](https://bioconductor.org/packages/WeberDivechaLCdata)) or directly [here](https://bioconductor.org/packages/release/data/experiment/vignettes/WeberDivechaLCdata/inst/doc/WeberDivechaLCdata.html).
## 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](https://elifesciences.org/articles/84628), 12:RP84628.