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This is the development version of pipeComp; for the stable release version, see pipeComp.

pipeComp pipeline benchmarking framework

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

pipeComp HTML R Script
pipeComp_dea HTML R Script
pipeComp_scRNA HTML R Script
Reference Manual PDF


biocViews Clustering, DataRepresentation, GeneExpression, Software, Transcriptomics
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
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Follow Installation instructions to use this package in your R session.

Source Package pipeComp_1.15.0.tar.gz
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macOS Binary (x86_64) pipeComp_1.15.0.tgz
macOS Binary (arm64) pipeComp_1.15.0.tgz
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