pipeComp

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see pipeComp.

pipeComp pipeline benchmarking framework

Bioconductor version: 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 (!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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, DataRepresentation, GeneExpression, Software, Transcriptomics

Version 1.0.0

In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)

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

System Requirements

URL https://doi.org/10.1186/s13059-020-02136-7

Bug Reports https://github.com/plger/pipeComp

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