pipeComp

DOI: 10.18129/B9.bioc.pipeComp    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see pipeComp.

pipeComp pipeline benchmarking framework

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("pipeComp")

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

Documentation

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

browseVignettes("pipeComp")

 

HTML	R Script	pipeComp
HTML	R Script	pipeComp_dea
HTML	R Script	pipeComp_scRNA
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, DataRepresentation, GeneExpression, Software, Transcriptomics
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
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
LinkingTo
Suggests	BiocStyle, rmarkdown
SystemRequirements
Enhances
URL	https://doi.org/10.1186/s13059-020-02136-7
BugReports	https://github.com/plger/pipeComp
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	pipeComp_1.2.0.tar.gz
Windows Binary	pipeComp_1.2.0.zip
macOS 10.13 (High Sierra)	pipeComp_1.2.0.tgz
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