Spatial epigenomics in FFPE tissues

This repository documents scripts used for data analysis and visualization in our manuscript entitled 'Spatially Decoding Genotype-Associated Epigenetic Landscapes in Human Lymphoma FFPE Tissues via epi-Patho-DBiT', where we developed a platform that combines reverse crosslinking of FFPE tissues with spatially resolved assays for transposase-accessible chromatin using sequencing (spatial-FFPE-ATAC) or cleavage under targets and tagmentation (spatial-FFPE-CUT&Tag).

general - repository of scripts for general data processing and analysis

1. Fragment file processing and spatial barcode mapping in Python (SnapATAC2)
2. Fragment data QC and clustering analysis in Python
3. Gene activity computation and differential analysis in Python
4. General data visualization scripts
5. Fragment file processing and peak calling in R (Signac)
6. Fragment data QC and visualization in R
7. Motif analysis with chromvar in R
8. Visuazation of SPOTlight deconvolution outputs
9. Cross-sample comparison related to Figure 1

lymphoma - repository of scripts for human lymphoma data analysis

1. Tissue architecture super-resolution inference using iStar, including input file preparation in Python, iStar bash scripts and a mask tissue image
2. Copy number variation inference using epiAneufinder, including epiAneufinder analysis in R and downstream analysis in Python
3. Cell cycle scoring and gene module scoring analysis
4. Trajectory inference with Monocle2 and Monocle3
5. Mitotic age inference with Epitrace, including Epitrace analysis in R and downstream analysis in Python
6. Analysis of Patho-DBiT (spatial-RNA-seq) data, including dimension reduction/clustering in Scanpy and inferCNV analysis in R
7. Spatial cell-cell interaction analysis with NICHES in R
8. Visualization of fragment data with circos