R codes for downstream analysis of “Deciphering transcriptome alterations in bone marrow hematopoiesis at single-cell resolution in immune thrombocytopenia”. Details of scripts in each folder:
1.Seurat_HSPCs folders contain codes for quality control, single cell clustering, differentially expressed genes identification and cellular composition anaysis of HSPCs.
2.Monocle folder includes codes for trajectory analyses using Monocle2 R package.
3.PAGA folder includes codes for trajectory analyses using PAGA.
4..SCENIC folder includes codes for transcription factor and gene co-expression network construction, regulon activity of each single cell of HSPCs, and differential regulon activity analysis.
5.Cell-cell_interaction folder contains the scripts for downstream analysis of the output of cellphoneDB, a package for infering cell to cell communication.
Contact: Yan Liu ([email protected])