CITEVizTestData is an ExperimentHub package that contains two CITE-Seq datasets from peripheral blood mononuclear cells (PBMC). Each of the datasets are identical, but formatted as a Seurat or SingleCellExperiment object. Each object contains 2500 cells and 228 antibodies, and is a down-sampled version of the data by Hao et. al. 2021 under the Creative Commons BY 4.0 license. Users can have the choice to download the data in either format and export it as an RDS file for use with CITEViz. For more information about CITEViz, please click here.
While there are multiple ways to download data from ExperimentHub (more info in the CITEVizTestData vignette), below is one such example:
library(ExperimentHub)
# create EH instance and query it
eh <- ExperimentHub()
query_results <- query(eh, "CITEVizTestData")
# get PBMC CITE-Seq datasets in two formats
file_seurat <- query_results[["EH7739"]] # Test data in Seurat format
file_sce <- query_results[["EH7740"]] # Test data in SingleCellExperiment format
The next step is to export the data to an RDS file, which can be uploaded to CITEViz via the upload button in the GUI.
# export information to external file
saveRDS(file_seurat, "pbmc-cite-seq-2500-seurat.rds")
saveRDS(file_sce, "pbmc-cite-seq-2500-sce.rds")