Spectral entropy

Spectral entropy is an application of Shannon entropy from information theory (1, 2).
Please view for more documentation.
Brief steps:

1. Create reference file with ./makeCustomGenomeSizes.sh ; change species, blacklist_path, and telomere_path ; if using hg38, you can use /new-stg/home/eunice_2/Entropy/00_LocalKL/18_new/hg38_res.3000.bed_res.3000.bed.size.200.bed and skip this step.
2. Create pseudobulks using ./PrepareCells.R ; change the seurat_path, conditions, and cell_ parameters with the path to your seurat object, meta column with conditions i.e. AD vs Control, and meta column with celltype labels, respectively.
3. sbatch head.sh ; change the inputdir with the output directory from PrepareCells.R ; set the outputdir with the output directory path ; set the codedir with the directory with all the copied script ; all outputs are saved in the outputdir variable.

References

1. Shannon, C. E. A mathematical theory of communication. Bell Syst. Tech. J. 27, 379–423 (1948).
2. Li, Y., Kind, T., Folz, J. et al. Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification. Nat Methods 18, 1524–1531 (2021).