scRNA-seq analysis of toxoplasma-infected cortical brain organoids

The code and the data in this repository enables the reproduction of the analyses and plots for the single-cell RNA-seq data in the paper "Engineering a Brain Parasite for Intracellular Delivery of Proteins to the Central Nervous System" (CELL-D-23-00107).

Filtering and Annotation

Initial processing of the dataset: quality metrics, filtering, normalization, dimensionality reduction, clustering and celltype annotation.

Markers

Plots of the markers for the relevant cell populations.

Differential Analysis

Computation and functional annotation of the differentially expressed genes.

MECP2 Related Genes

Plots of the expression of MECP2-related genes.