Question: Parallelize consensusClusterPlus package
gravatar for manali.rupji
2.7 years ago by
United States
manali.rupji10 wrote:

Hi All,

I am using consensus cluster package as a part of a shiny tool for genomic data. This package runs on my local machine in about a minute but takes almost 15-20 mins to run on the virtual machine instance. What are the possible solutions to increase the computational speed of the package? Is parallelism possible? Cr could it be the configuration the shiny servers causing the package to slow down?

I tried decreasing the number of reps in the package( from 100 to 50), but on the server, I still don't see any improvement in the processing time.

Could anyone also suggest alternate R packages for fast cluster analysis for normalized RNASeq data.

Greatly appreciate any help in this regard.

Regards, M

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by manali.rupji10

Check you're not running out of memory on the server.

ADD REPLYlink written 2.7 years ago by Jean-Karim Heriche23k
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