pipeComp

DOI: 10.18129/B9.bioc.pipeComp    

This is the development version of pipeComp; to use it, please install the devel version of Bioconductor.

pipeComp pipeline benchmarking framework

Bioconductor version: Development (3.12)

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 "4.0") and enter:

if (!requireNamespace("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

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 0.99.61
In Bioconductor since BioC 3.12 (R-4.0)
License GPL
Depends R (>= 4.0)
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
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_0.99.61.tar.gz
Windows Binary pipeComp_0.99.61.zip (32- & 64-bit)
macOS 10.13 (High Sierra) pipeComp_0.99.61.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: