Integrative spatial and single cell analyses of pre-cancerous cervical disease reveal key epithelial and macrophage interplay for AI-assisted non-Invasive triage

This is the code repository, including spatially-aware single cell analytical pipeline (SApipe) and multi-omic codes for cervical intraepithelial neoplasia project. In this progect, we assembled a large multi-stage cohort and used multi-omic analysis to unravel cerivcal carcinogenesis.

Raw sequencing data is submitted to Genome Sequence Archive at the National Genomics Data Center (Beijing, China) under ID: PRJCA048591 (HRA014027). To facilitate community access, we built an interactive website (http://meta-cancer.cn/cin/) to visualize and analyze our data. The code for spatially-aware single cell analytical pipeline and reproducing major figures is available on GitHub (https://github.com/Whistick/SApipe_and_CINcode). Any additional information required to re-analyze the data reported in this paper is available from the lead contact upon request.