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本代码关联于论文《疟原虫肝阶段时空分辨单细胞图谱》。 本研究生成的数据已提交至基因表达综合数据库（Gene Expression Omnibus，GEO），收录号为GSE181725。用于将原始数据处理为分析所用Scanpy/Seurat结构的代码，可从https://github.com/AmichayAfriat/SpatioTemporal_malaria_liver_stage_atlas/获取。 本仓库中包含已处理的单细胞RNA测序（single-cell RNA sequencing, scRNAseq）数据，以及用于后续分析与数据可视化的代码。代码采用R（4.0.2版本，依赖包包括seurat、dplyr、tidyr、ggpubr、stats及EnhancedVolcano）与MATLAB（2019a版本）编写。 文件夹：附加数据 分析中所用的元数据 NZ_data.txt：通过'analyze_neighborhood_intensity.m'函数从单分子荧光原位杂交（single-molecule fluorescence in situ hybridization, smFISH）图像中提取的分区数据 文件夹：图表源数据 论文图表中图形展示所基于的数据 每个文件均包含针对不同子图的清晰标注工作表 文件夹：函数 Matlab脚本中所用的函数 文件夹：GSEA_OUTPUT 基因集富集分析（Gene Set Enrichment Analysis, GSEA，v3.0）输出结果。 采用经过整理的京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）及HALLMARK注释集进行分析。 筛选条件为：基因集内基因数不少于15且不超过500。默认采用1000次置换以确定显著性水平。针对流产型细胞的差异基因表达（Differential Gene Expression, DGE）分析使用了更严格的阈值：相对表达量>10^-4，且基因集内最少包含30个基因。