RESOURCE

Wet-lab

1. Protocol of RDD: a detailed protocol and quality control results of RDD library construction.

2. Protocol of Tn5-Labeled DNA-FISH: an Optimized Probe Preparation Method for Probing Genome Architecture.

3. Protocol of TF-chRDP: a method for simultaneously capturing transcription factor binding chromatin-associated RNA, DNA and protein.

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Dry-lab

1. MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification, includes MCI-view and MCI-2kde two parts.

2. MCI-frcnn: a deep learning based object detector used for micro-domain boundary detection.

3. ScSmOP: a general-purpose pipeline that works for processing the “one barcode one group” type of state-of-art multiomics data.

4. scAIR-pipeline: a specifically coded for scAIR (single cell ATAC/Interactome/RNA) methods, based on ScSmOP GitHub.

5. roX2-RDD data analysis: a wiki to present our approaches to data processing, analysis, and visualization in the study of the roX2-RDD.

6. EBV-RDD figure script: all scripts used to generate the source data figures of EBV-RDD article

7. EBV 3D model: visualization of 3D modeling EBV’s genome.