So I'm trying to integrate two datasets together for 10 different samples (taken in different batches). To mitigate for that I looked into Harmony but was not sure how to essentially apply Harmony from two datasets and get fragment files for later analysis in ArchR.

Any suggestions or pointers?
`ArchR` has built-in support for Harmony correction; 

```
projHeme2 <- addHarmony(
    ArchRProj = projHeme2,
    reducedDims = "IterativeLSI",
    name = "Harmony",
    groupBy = "dataset"
)
```

https://www.archrproject.com/bookdown/batch-effect-correction-wtih-harmony.html