These are the codes used in the article entitled "Docoding the cTRN govering wheat inflorescence development with spatiotemporal resolution"
To run these codes, you need to install R packages Seurat(v4.3.0), ArchR (v1.0.3), tidyverse, Monocle3, sctransform, BSgenome
snRNA.r: code used for snRNA-seq data analysis. snATAC.r: code used for snATAC-seq data analysis. Tangram.py: code used for scStereo-seq data analysis. Monocle3.r: code used for trajectory inference.
The 'Test' folder contains test data, test code, and test results. For snRNA-seq: 'snRNA.TestData' folder contains input data for snRNA-seq analysis test. snRNA.test.r: test code for snRNA-seq data anslysis. 'test.snRNA.celltype.specific.genes.txt' and 'test.snRNA.Seurat.rds' are the results for snRNA-seq data analysis test.
For snATAC-seq: 'test.snATAC.fragment.tsv.gz' and 'test.snATAC.fragment.tsv.gz.tbi' are the input data for snATAC-seq analysis test. snATAC.test.r: test code for snATAC-seq data analysis. 'test.snATAC.output' folder contains the results for snATAC-seq data analysis test.