Hi all,
After reading materials about how to analyzing single-cell multiome, I am not sure how to analyze them correctly. I have two data set: normal (healthy cells only) vs diseased (healthy cells differential into other cell type and may not function). I try to find which transcription factors cause the different in phenotype, so I use these vignettee:
https://satijalab.org/seurat/articles/weighted_nearest_neighbor_analysis
https://satijalab.org/seurat/articles/atacseq_integration_vignette
https://stuartlab.org/signac/articles/pbmc_multiomic.html
I group all cells that come from the same cluster and try to get TPM value to compare between two conditions, can't perform pseudobulk RNA-seq because I don't have replicates.
I found some papers that perform these analyses and try to follow but not sure about some steps. Their code in github is quite complex.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9296597/#MOESM1
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8990373/
Would you please have a suggestion for this? I really appreciate your input!
