Bibliography

Methods & software

• ArchR — analysis of single-cell chromatin accessibility data. https://www.archrproject.com/
• SnapATAC2 — scalable single-cell epigenomics analysis. https://github.com/kaizhang/SnapATAC2
• SpatialGlue — spatial multi-omics integration. https://github.com/JinmiaoChenLab/SpatialGlue
• STAGATE — spatial clustering via graph attention auto-encoders. https://github.com/zhanglabtools/STAGATE

Primary literature

• Deng, Y. et al. High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. Cell 183, 1665–1681 (2020).
• Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Science 375(6581), 681–686 (2022).
• Spatial profiling of chromatin accessibility in mouse and human tissues. Nature 609, 375–383 (2022).
• Spatial epigenome–transcriptome co-profiling of mammalian tissues. Nature 616, 113–122 (2023).