A spatiotemporally resolved single cell atlas of the Plasmodium liver stage

This code is associated with the paper "A spatiotemporally resolved single cell atlas of the Plasmodium liver stage"

Data generated in this study have been deposited in Gene Expression Omnibus with the accession code GSE181725. The code used to process the raw data to a Scanpy/Seurat structure used for analysis is available at https://github.com/AmichayAfriat/SpatioTemporal_malaria_liver_stage_atlas/.

In this repository, you will find processed scRNAseq data and the codes used for further analysis and data visualization. Codes written in R (4.0.2; packages include seurat, dplyr, tidyr, ggpubr, stats, and EnhancedVolcano) and MATLAB (2019a).

Folder: Additional data

Metadata used in the analysis

NZ_data.txt - Zonation data extracted from smFISH images using the 'analyze_neighborhood_intensity.m' function 

Folder: Figures_source_data

Data underlying the graphical representations used in figures

Each file contains clearly labeled sheets for distinct subplots

Folder: functions

Functions used in Matlab scripts

Folder: GSEA_OUTPUT

Gene Set Enrichment Analysis (GSEA, v3.0) output.

Curated KEGG and HALLMARK annotations were used

Filtered for minimum 15 genes in set and maximum 500. Default setting of 1,000 permutation was used to establish significance. For abortive cells DGE stricter thresholds were used - relative expression > 10-4, and minimum 30 genes in set