pipeComp: pipeComp pipeline benchmarking framework

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.

Package details

AuthorPierre-Luc Germain [cre, aut] (<https://orcid.org/0000-0003-3418-4218>), Anthony Sonrel [aut] (<https://orcid.org/0000-0002-2414-715X>), Mark D. Robinson [aut, fnd] (<https://orcid.org/0000-0002-3048-5518>)
Bioconductor views Clustering DataRepresentation GeneExpression Transcriptomics
MaintainerPierre-Luc Germain <pierre-luc.germain@hest.ethz.ch>
URL https://doi.org/10.1186/s13059-020-02136-7
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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pipeComp documentation built on Nov. 8, 2020, 7:35 p.m.