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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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speed up addClusters #2166

Open limiao20 opened 6 months ago

limiao20 commented 6 months ago

I am using the addClusters function with method = "Seurat" and resolution = 0.8. While clustering 9 samples takes approximately 9 hours, clustering 35 samples has already taken over 180 hours. Is this computation time reasonable? Are there any optimizations or alternative methods within ArchR to speed up this step? Thank you for your assistance.

rcorces commented 6 months ago

Hi @limiao20! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.