Package: pipeComp
Type: Package
Title: pipeComp pipeline benchmarking framework
Version: 1.23.5
Depends: R (>= 4.1)
Authors@R: c(
	person("Pierre-Luc", "Germain", email="pierre-luc.germain@hest.ethz.ch", role=c("cre","aut"), comment = c(ORCID = "0000-0003-3418-4218")), 
	person("Anthony", "Sonrel", email="anthony.sonrel@uzh.ch", role="aut", comment = c(ORCID = "0000-0002-2414-715X")), 
	person("Mark D.", "Robinson", email="mark.robinson@imls.uzh.ch", role=c("aut","fnd"), comment = c(ORCID = "0000-0002-3048-5518")) )
Description: 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.
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
License: GPL
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://doi.org/10.1186/s13059-020-02136-7
BugReports: https://github.com/plger/pipeComp
biocViews: GeneExpression, Transcriptomics, Clustering,
        DataRepresentation
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libuv1-dev libwebp-dev libxml2-dev libssl-dev perl python3
        libnode-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-13 14:45:06 UTC
RemoteUrl: https://github.com/bioc/pipeComp
RemoteRef: HEAD
RemoteSha: 35be0e31a90b5b987c0805f709cecdc3ba92e7d2
NeedsCompilation: no
Packaged: 2026-06-13 15:36:59 UTC; root
Author: Pierre-Luc Germain [cre, aut] (ORCID:
    <https://orcid.org/0000-0003-3418-4218>),
  Anthony Sonrel [aut] (ORCID: <https://orcid.org/0000-0002-2414-715X>),
  Mark D. Robinson [aut, fnd] (ORCID:
    <https://orcid.org/0000-0002-3048-5518>)
Maintainer: Pierre-Luc Germain <pierre-luc.germain@hest.ethz.ch>