scEiaD

Harmonize publicly available scRNA-seq datasets for the eye

The code base that underlies the data for plae.nei.nih.gov

Version 0.92

Selected parameters for integration

• scANVI (scVI version 0.13)
• 4000 HVG
• 5 epochs
• 15 latent dimensions

Yaml files

• config.yaml for SnakeQUANT and SnakePOP
• configSCEIAD.yaml for SnakeSCEIAD

Numbers

• 44 datasets
• 4 species (human, mouse, macaque, chicken)
• 1,136,041 cells
• ~60 different cell types

<img width="329" alt="image" src="https://user-images.githubusercontent.com/10225430/189389690-13381192-79fa-48df-945f-8a439bcfcb09.png">

Data

• scEiaD database for PLAE
• Seurat (v3)
• anndata (h5ad)
• Cell Level Metadata
• Cell Level Metadata in FST format used by web app
• Counts (Rdata sparse matrix)

Moar data?

Visit plae.nei.nih.gov -> Data for differential gene expression tables, study level counts, and more.

How do I add my own data to scEiaD?

It is possible! Even better, you don't have to ask me! Or tell me!

Interactive colab notebook