How to make DiffBind Run Faster?

Question

[B.N.]

Wondering how to make diffbind run faster. Am on an RStudio server on a linux machine. I set bParallel = TRUE in dba.count(). However, it still seems to be taking a very long time. I notice it's only using 1.5 to 2 GB of RAM max. Is there any way I can further optimize this and make it utilize more RAM? Also, is there any way to see how many cores it's utilizing and make it use more cores too?

Answer 1

[jared.andrews07]

Set the number of cores for your dba object. For example, if your dba object is named tamoxifen:

tamoxifen$config$cores <- 12

Note the parallelization in DiffBind does not work on Windows.

You might also give csaw a try, as it's much quicker and generally more flexible (though as a result requires more adjustments and thought).