This is the development version of pipeComp; for the stable release version, see pipeComp.
pipeComp pipeline benchmarking frameworkBioconductor version: Development (3.22)
A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.
Author: Pierre-Luc Germain [cre, aut] ORCID: 0000-0003-3418-4218 , Anthony Sonrel [aut] ORCID: 0000-0002-2414-715X , Mark D. Robinson [aut, fnd] ORCID: 0000-0002-3048-5518
Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>
Citation (from within R, entercitation("pipeComp")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("pipeComp")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pipeComp")Follow Installation instructions to use this package in your R session.
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