pipeComp
pipeComp pipeline benchmarking framework
Bioconductor version: 3.24 · Package version: 1.23.5
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pipeComp")Details
| Maintainer | Pierre-Luc Germain <pierre-luc.germain@hest.ethz.ch> |
| 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>) |
| License | GPL |
| URL | https://doi.org/10.1186/s13059-020-02136-7 |
| Bug Reports | https://github.com/plger/pipeComp |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DataRepresentation, GeneExpression, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/pipeComp/ |
Citation
From within R, enter citation("pipeComp"):
Pierre-Luc Germain, Anthony Sonrel, Mark D. Robinson. pipeComp: pipeComp pipeline benchmarking framework. doi:10.18129/B9.bioc.pipeComp, R package version 1.23.5, https://bioconductor.org/packages/pipeComp.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | pipeComp_1.23.5.tar.gz |
| Windows binary (x86_64) | pipeComp_1.23.5.zip |
| macOS binary (arm64) | pipeComp_1.23.5.tgz |
| macOS binary (x86_64) | pipeComp_1.23.5.tgz |
Dependencies
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