pipeComp

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

pipeComp pipeline benchmarking framework

Bioconductor version: Development (3.19)

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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("pipeComp")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, DataRepresentation, GeneExpression, Software, Transcriptomics
Version	1.13.0
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
System Requirements
URL	https://doi.org/10.1186/s13059-020-02136-7
Bug Reports	https://github.com/plger/pipeComp

Suggests	BiocStyle, rmarkdown
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Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/pipeComp
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pipeComp
Package Short Url	https://bioconductor.org/packages/pipeComp/
Package Downloads Report	Download Stats