Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.
Number of sets: 6 cell types direction (3) 2 assays (ATAC and RNA) = 36 sets
Note: snATAC-seq and snRNA-seq
[ ] (low priority since it's ATAC-seq with no assigned genes) Table S5: try it with and without direction
Direction available: avg_logFC
Statistics available: p_val_adj
Genes are not assigned. We have the Peak coordinates. We could use GenomicRanges::findOverlaps() to compare against the annotation.
[ ] Let's try subsetting to Peaks that overlap a single gene first (including the UTRs). If they don't overlap genes or overlap to 2 or more genes, we'll ignore them. But it could be that we lose too many peaks that way.
[ ] Another option is to find the distance to the closest 5' of a gene. Maybe with a maximum distance filter.
[x] Table S1: split by celltype, try it with and without direction
Number of sets: 6 cell types direction (3) 2 assays (ATAC and RNA) = 36 sets
Note: snATAC-seq and snRNA-seq
[ ] (low priority since it's ATAC-seq with no assigned genes) Table S5: try it with and without direction
avg_logFCp_val_adjPeakcoordinates. We could useGenomicRanges::findOverlaps()to compare against the annotation.Peaks that overlap a single gene first (including the UTRs). If they don't overlap genes or overlap to 2 or more genes, we'll ignore them. But it could be that we lose too many peaks that way.celltype, try it with and without directionavg_logFCp_val_adj(looks filtered already)