This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
For further information about this project, please contact:
This project uses 10X Genomics Epi multiome single cell data to identify mechanisms that drive cell-cell transitions during human retinal development. Analysis tools used are primarily from the scverse ecosystem of software tools (scverse.org). ONT long-read 10X single cell RNAseq will also be implemented.
The following software will be used in this project.
* General programming: Python 3 and R.
* 10X genomics scRNA-seq analysis software: CellRanger and SpaceRanger.
* Downstream scRNA-seq: ScanPy, Muon, EpiTrace, pseudotime, RNA velocity and LIANA.
* ONT long read analysis: EPI2ME, nf-core/scnanoseq.
Where possible pipelines will make use of the GPU-accelerated nodes for large analysis workloads.