Controlling Donor and Newborn Neuron Migration and Maturation in the Eye Through Microenvironment Engineering

In this repository you may find the information for reproducing the bioinformatical analysis of human fetal, organoids and adult retina datasets.

The analysis in this study includes:

1. R-Seurat datasets processing and de novo annotation
2. GSEA pathway analysis
3. Migration patterns search
4. Python-ForceAtlas2 transformation (scanpy, scFates) and migration-maturation correlation

Files for reproducing the analysis: retina_singlecell.R, retina_scfates.ipynb, RGC_fetal_merged.ipynb.

The processed datasets are available here.

For any questions, suggestions and ideas, send an e-mail to:

1. Jonathan R Soucy, jonathan_soucy@meei.harvard.edu, corresponding author
2. Petr Baranov, petr_baranov@meei.havard.edu, corresponding author, PI
3. Emil Kriukov, ekriukov@meei.harvard.edu, bioinformatics

Paper preprint is available on bioRxiv.