CellOracle

分析流程

1. ATAC-seq data preprocessing

目的： identify accessible promoter/enhancer DNA regions

scATAC-seq: proximal and distal promoter/enhancer genome sequences(co-accessible socres and TSS infomation)

bulk ATCC seq: proximal promoter/enhancer genome sequences

输入：ATAC的结果，以bed file的形式

输出：peaks,gene_short_name,co-access scores(bulk无)

2. Transcription factor binding motif scan

目的： 扫描基因的调控序列，获取TF list
输出：矩阵，行peaks name and target gene name, 列TF names

3. scRNA-seq data preprocessing with scanpy or seurat

4. Network analysis