In SydneyBioX/scMerge: scMerge: Merging multiple batches of scRNA-seq data

Introduction

This is a human breast cancer single-cell data comprising of 4 different batches from a single experiment.

Integration challenge

Prior to integration, there is a strong separation effect by batches.
With 24,520 cells, this data poses dimensionality challenge to data integration.

Data description

Data source:

| Type of merge | | Name | | ID | Author | DOI or URL | Protocol | Organism | Tissue | # of cell types | # of cells | # of batches | |---------------|---|--------|---|-----------|--------|----------------------------|--------------|----------|---------------|-----------------|------------|--------------| | Within experiment | | Breast | | GSE113197 | Nguyen | 10.1038/s41467-018-04334-1 | 10x Chromium | Human | Breast cancer | 3 | 24520 | 4 |

Relation to the scMerge article: Supplementary Figure 7.

Data visualisation

tSNE plots by cell types and batch

Integrated `scMerge` data

Data availability: Breast Data (in RData format)
scMerge parameters for integration:
- Unsupervised scMerge
- kmeans K = (4,3,4,3)
- Negative controls are human scSEG