BiocParallel v1.0.3
Bioconductor facilities for parallel evaluation
This package provides modified versions and novel
implementation of functions for parallel evaluation, tailored to
use with Bioconductor objects.
Readme
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"
Functions in BiocParallel
| Name | Description | |
| 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 | |
| No Results! | ||
Last year downloads
Details
| Type | Package |
| biocViews | Infrastructure |
| License | GPL-2 | GPL-3 |
| Collate.unix | AllGenerics.R BiocParallelParam-class.R ErrorHandling.R bpbackend-methods.R bpisup-methods.R bplapply-methods.R bpmapply-methods.R bpiterate-methods.R bpschedule-methods.R bpstart-methods.R bpstop-methods.R bpvec-methods.R bpvectorize-methods.R bpworkers-methods.R bpaggregate-methods.R DoparParam-class.R MulticoreParam-class.R register.R SerialParam-class.R SnowParam-class.R BatchJobsParam-class.R utilities.R unix/mclapply.R unix/pvec.R unix/bpiterate.R unix/zzz.R |
| Collate.windows | AllGenerics.R BiocParallelParam-class.R ErrorHandling.R bpbackend-methods.R bpisup-methods.R bplapply-methods.R bpmapply-methods.R bpiterate-methods.R bpschedule-methods.R bpstart-methods.R bpstop-methods.R bpvec-methods.R bpvectorize-methods.R bpworkers-methods.R bpaggregate-methods.R DoparParam-class.R MulticoreParam-class.R register.R SerialParam-class.R SnowParam-class.R BatchJobsParam-class.R utilities.R windows/zzz.R |
| VignetteBuilder | knitr |
| imports | BatchJobs , BBmisc , BiocGenerics , foreach , parallel , tools |
| suggests | BiocStyle , doParallel , GenomicAlignments , GenomicRanges , knitr , Rmpi , RNAseqData.HNRNPC.bam.chr14 , Rsamtools , RUnit , ShortRead , snow |
| depends | methods |
| Contributors | Bioconductor Package Maintainer, Michel Lang, Martin Morgan, Ryan Thompson |
Include our badge in your README
[](http://www.rdocumentation.org/packages/BiocParallel)