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BiocParallel

Bioconductor facilities for parallel evaluation (experimental)

Possible TODO

  • map/reduce-like function
  • bpforeach?
  • Abstract scheduler
  • lazy DoparParam
  • SnowParam support for setSeed, recursive, cleanup
  • subset SnowParam
  • elaborate SnowParam for SnowSocketParam, SnowForkParam, SnowMpiParam, ...
  • MulticoreParam on Windows
  • Short vignette

DONE

  • encapsulate arguments as ParallelParam()
  • Standardize signatures
  • Make functions generics
  • parLapply-like function

github notes

  • commit one-liners with names

    git log --pretty=format:"- %h %an: %s"

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Version

Version

1.0.3

License

GPL-2 | GPL-3

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in BiocParallel (1.0.3)

bpschedule

Schedule back-end Params
bpvec

Parallel, vectorized evaluation
BatchJobsParam-class

Enable parallelization on batch systems
BiocParallelParam-class

Virtual classes (for developer reference)
bpaggregate

Apply a function on subsets of data frames
bpcontrols

Control (start, stop, query) back-end Params
bpiterate

Parallel iteration over an indeterminate number of data chunks
bplapply

Parallel lapply-like functionality
bpmapply

Parallel mapply-like functionality
bpresume

Resume computation with partial results
SnowParam-class

Enable simple network of workstations (SNOW)-style parallel evaluation
SerialParam-class

Enable serial evaluation
MulticoreParam-class

Enable multi-core parallel evaluation
register

Maintain a global registry of available back-end Params
bpvectorize

Transform vectorized functions into parallelized, vectorized function
DoparParam-class

Enable parallel evaluation using registered dopar backend