scaeData

scaeData is an R/ExperimentHub data package designed to complement the functionality of the SingleCellAlleleExperiment R package.

The curated datasets found here were generated through the utilization of our dedicated scIGD Snakemake workflow. The workflow is an essential tool for producing the data required to seamlessly integrate with the SingleCellAlleleExperiment package.

The raw FASTQ files, constituting the foundation of these datasets, were sourced from publicly available datasets provided by 10x Genomics.

scaeData consists of 3 single-cell RNA-sequencing datasets:

• 5k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor (v3 chemistry)

• 10k Human PBMCs, 3' v3.1, Chromium Controller

• 20k Human PBMCs, 3' HT v3.1, Chromium X

Installation

scaeData is available in Bioconductor and can be installed as follows:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

BiocManager::install("scaeData")

Alternatively, it can be installed from GitHub using the devtools package:

if (!require("devtools", quietly = TRUE))
    install.packages("devtools")

devtools::install_github("AGImkeller/scaeData", build_vignettes = TRUE)

About

Please consult scIGD and SingleCellAlleleExperiment documentations for more details.

Bugs and issues

Please report any bugs and/or issues to the scIGD Issues page

Citation

Authors

• Ahmad Al Ajami, Jonas Schuck, Federico Marini, Katharina Imkeller