HCATonsilData: Access the Tonsil Atlas data (RNA, ATAC, Multiome, CITE,...

In massonix/HCATonsilData: Provide programmatic access to the tonsil cell atlas datasets

Access the Tonsil Atlas data (RNA, ATAC, Multiome, CITE, Spatial)

Description

The data was downloaded from Zenodo https://zenodo.org/record/8373756

Usage

HCATonsilData(
  assayType = c("RNA", "ATAC", "CITE", "Spatial"),
  cellType = "All",
  version = "2.0",
  processedCounts = TRUE
)

Arguments

assayType	One of 'RNA', 'ATAC', 'Multiome', 'CITE' or 'Spatial'.
cellType	A character vector of length 1 with the desired cell type. A list of available cell types can be obtained using listCellTypes(assay_type).
version	Version of the tonsil atlas data to retrieve: "1.0" (preprint) or "2.0" (publication, default)
processedCounts	Logical scalar. If TRUE, include the processed (normalized) counts in addition to the raw counts in the SingleCellExperiment object.

Value

A SingleCellExperiment object for the cellType requested. For scATAC-seq, Multiome and CITE we provide the instructions for downloading the Seurat objects in Zenodo (see vignette)

Author(s)

Ramon Massoni-Badosa

Examples

# retrieve the epithelial scRNA-seq dataset
sce_epithelial <- HCATonsilData(
  assayType = "RNA",
  cellType = "epithelial"
)
sce_epithelial

massonix/HCATonsilData documentation built on Nov. 1, 2023, 10:33 a.m.