ASCAL Pipeline Maps the Mouse Ocular Atlas and RAO Dynamics

ASCAL (Automated Single-Cell Annotation and Localization) is a pipeline for integrated analysis of mouse eyes' SeekSpace, Stereo-seq, and scRNA-seq data to construct the mouse ocular atlas and decode RAO disease dynamics.

Source Code Organization

The workflows were implemented and managed using Snakemake.

1. seekspace: Manul annotation of SeekSpace data (major cell types and sub-Rods).
2. stereoseq: Data processing of Stereo-seq at bin50 resolution.
3. WT_retina_cb_scRNAseq: eClassifer applied in scRNA-seq of retina and ciliary body (cb).
4. Apoe_KO_retina_scRNAseq: eClassifer applied in CON/RAO scRNA-seq of Apoe KO mouse retina.
5. cell2location: Cell localization prediction based on Stereo-seq data.
6. compare_unsupervised: Compare eClassifer with unsupervised methods.
7. compare_other_tools: Compare eClassifer with other tools.

Developers

• Chen Du
• Yijie Wang

Softwares

1. CytoSpace
2. TopACT
3. SeekSpace® Tools (version=1.0.0)
4. SAW (https://github.com/STOmics/SAW)

R packages

1. Seurat (version=4.3.0)
2. RCTD
3. e1071
4. ggplot2

Conda environment

• env.yaml