text: user2005: I need to implement a parallel version of an R script because on one core it takes forever to execute. The function that takes the most of time is scran::quickCluster() applied to an integer sparse matrix (UMI_count) that is 26000x66000. The code is presented below:
  library(scran)
  library(scater)
  sce <- newSCESet(countData=UMI_count)
  clusters <- quickCluster(sce)
  sce <- computeSumFactors(sce, cluster=clusters)
  
  I did not find much on parallel versions of quickCluster() function, so will it actually execute in parallel if I set the number of cores to more than one? I am trying to do normalization of heterogeneous dataset with multiple cell types, that is why I am using quickCluster().
  And I just need to speed it up to be able to compute it.
  
  user900: The scran::quickCluster method has a BPPARAM (i.e., BiocParallelParam), so if one provides something like
  clusters <- quickCluster(sce, BPPARAM=BiocParallel::MulticoreParam())
  
  it will use all available cores (a specific number of cores can also be given). See the intro doc to BiocParallel for info on other options.
  
original_text: 2005: <p>I need to implement a parallel version of an R script because on one core it takes forever to execute. The function that takes the most of time is <code>scran::quickCluster()</code> applied to an integer sparse matrix (<code>UMI_count</code>) that is <code>26000x66000</code>. The code is presented below:</p>
  
  <pre><code>library(scran)
  library(scater)
  sce &lt;- newSCESet(countData=UMI_count)
  clusters &lt;- quickCluster(sce)
  sce &lt;- computeSumFactors(sce, cluster=clusters)
  </code></pre>
  
  <p>I did not find much on parallel versions of <code>quickCluster()</code> function, so will it actually execute in parallel if I set the number of cores to more than one? I am trying to do normalization of heterogeneous dataset with multiple cell types, that is why I am using <a href="https://bioconductor.org/packages/release/bioc/vignettes/scran/inst/doc/scran.html" rel="nofollow noreferrer"><code>quickCluster()</code></a>.</p>
  
  <p>And I just need to speed it up to be able to compute it.</p>
   900: <p>The <a href="https://rdrr.io/bioc/scran/man/quickCluster.html" rel="nofollow noreferrer"><code>scran::quickCluster</code> method</a> has a <code>BPPARAM</code> (i.e., <code>BiocParallelParam</code>), so if one provides something like</p>
  
  <pre><code>clusters &lt;- quickCluster(sce, BPPARAM=BiocParallel::MulticoreParam())
  </code></pre>
  
  <p>it will use all available cores (a specific number of cores can also be given). See <a href="https://bioconductor.org/packages/devel/bioc/vignettes/BiocParallel/inst/doc/Introduction_To_BiocParallel.pdf" rel="nofollow noreferrer">the intro doc to <code>BiocParallel</code></a> for info on other options.</p>
  