What's the STARK? =================== .. image:: _static/stark_logo.png :width: 300px sc3DG-seq has emerged as an essential tool for understanding the variability in 3D chromatin structure among individual cells. The process encompasses cell sorting, chromosome cross-linking, digestion, ligation, and sequencing, culminating in a map of interactions across the genome. Despite the development of over ten distinct sc3DG-seq techniques, each with unique processing requirements, a unified computational framework has been lacking. This gap poses a significant challenge to the research community, hindering the effective utilization of these extensive and valuable data. To address this challenge, we propose STARK, a unified framework that conducts preprocessing, quality control and downstream analysis for all current sc3DG-seq data types (Fig S1). STARK encompasses three modules: Preprocess, Cell QC (Quality Control) and Downstream Analysis. STARK is a software for processing various types of sc3DG-seq sequencing data, which currently includes the sc3DG-seq technologies as follows: * scHi-C (`Nagano et al., 2013 `_) * scHi-C+ (`Argelaguet et al., 2019 `_) * Dip-C (`Tan et al., 2018 `_) * HiRES (`Wang et al., 2023 `_) * sn-m3C (`Lee et al., 2019 `_) * scSPRITE (`Quinodoz et al., 2018 `_) * sciHi-C (`Ramani et al., 2017 `_) * snHi-C (`Lee et al., 2019 `_) * scNanoHi-C (`Lee et al., 2022 `_) * scMethyl-HiC (`Li et al., 2019 `_)