pipeComp
pipeComp pipeline benchmarking framework
Bioconductor version: Release (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("pipeComp")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Clustering, DataRepresentation, GeneExpression, Software, Transcriptomics |
Version | 1.14.0 |
In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.14.0.tar.gz |
Windows Binary | pipeComp_1.14.0.zip |
macOS Binary (x86_64) | pipeComp_1.14.0.tgz |
macOS Binary (arm64) | pipeComp_1.14.0.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 |