Coralysis Vignettes SCE Objects

This repository contains SingleCellExperiment (SCE) objects used for running Coralysis vignettes. The purpose of this repository is to facilitate the distribution of medium-to-large-sized SCE objects compatible with Coralysis, allowing users to reproduce various vignettes. All datasets shared through this repository were originally made public by their respective authors, who are properly acknowledged herein, with links to the original publications.

File description: 

pbmc_10Xassays.rds: Two 10X PBMCs 3' assays, V1 and V2, downsampled to 2K cells (1K per assay). Both datasets have been downloaded from 10X website (see source below). The PBMC dataset V1 corresponds to sample pbmc6k and V2 pbmc8k. Cells were annotated using the annotations provided by Korsunsky et al., 2019 (PMID:31740819; Source Data Figure 4 file).

V1: pbmc6k

V2: pbmc8k

covid_Wilk_et_al.rds: Single-cell RNA sequencing atlas of peripheral blood mononuclear cells (PBMCs) from healthy versus COVID-19 infected donors published by Wilk et al., 2020 (PMID:32514174). In addition, the object provides the cell type annotations given by Välikangas et al., 2022 (PMID:35991542). The original dataset has been downsampled to 21K cells (1.5K cells per Donor_full sample; from 44,721 cells) to increase the speed and reduce the computational resources required to reproduce the vignette.