Welcome to the new bioconductor.org!

pipeComp

pipeComp pipeline benchmarking framework


Bioconductor version: Release (3.18)

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 "4.3") and enter:


if (!require("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")
pipeComp HTML R Script
pipeComp_dea HTML R Script
pipeComp_scRNA HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, DataRepresentation, GeneExpression, Software, Transcriptomics
Version 1.12.0
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
See More
Suggests BiocStyle, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package pipeComp_1.12.0.tar.gz
Windows Binary pipeComp_1.12.0.zip
macOS Binary (x86_64) pipeComp_1.12.0.tgz
macOS Binary (arm64) pipeComp_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pipeComp
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pipeComp
Bioc Package Browser https://code.bioconductor.org/browse/pipeComp/
Package Short Url https://bioconductor.org/packages/pipeComp/
Package Downloads Report Download Stats