- Aim: to integrate single-cell RNA ovary datasets to build a transcriptomic ovary reference atlas.
- Objective: follow the methods used in hypoMap using online and in-house ovary datasets.
The hypoMap pipeline is split into three parts:
- Prepare datasets - downloading fastq files and SRA metadata, producing count matrices, and then creating Seurat objects from these.
- scIntegration - finding optimal hyperparameters for scVI to integrate datasets.
- scHarmonization - harmonising annotations for the integrated single cell dataset.
Follow the hypoMap pipeline.
- Prepare datasets
- Use the scIntegration scripts
- Use the scHarmonization scripts