DOI: 10.18129/B9.bioc.pipeComp  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see pipeComp.

pipeComp pipeline benchmarking framework

Bioconductor version: 3.17

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] , Anthony Sonrel [aut] , Mark D. Robinson [aut, fnd]

Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>

Citation (from within R, enter citation("pipeComp")):


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biocViews Clustering, DataRepresentation, GeneExpression, Software, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL
Depends R (>= 4.1)
Imports BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer
Suggests BiocStyle, rmarkdown
URL https://doi.org/10.1186/s13059-020-02136-7
BugReports https://github.com/plger/pipeComp
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Source Package pipeComp_1.10.0.tar.gz
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