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girke-lab / signatureSearch

R/Bioconductor package including the Gene Expression Signature Search (GESS), Function Enrichment Analysis (FEA) methods and supporting drug-target network construction for visualization
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Parallel execution of queries #1

Closed enricoferrero closed 4 years ago

enricoferrero commented 4 years ago

Hello,

Thanks for developing what looks like a great package.

I would like to run gess_lincs() across multiple queries in parallel. In the reference manual it is mentioned that this is possible, and I can see the BiocParallel package is imported when signatureSearchis loaded.

Can you please show a snippet of code detailing the recommended way to parallelise multiple queries?

Thank you, Enrico

yduan004 commented 4 years ago

Hi Enrico,

Thanks for your interest in the signatureSearch package. I have updated the vignette including a new section called Batch Processing of GESSs under the Signature Searches (GESS) section that addresses your need.

Please install the most updated package (version 1.1.4) from github by running

devtools::install_github("yduan004/signatureSearch", build_vignettes=TRUE)

If the building vignette process failed, please set build_vignettes as FALSE and reinstall.

If you have any questions, please feel free to ask me.

Thanks, Yuzhu