pipeComp
This is the development version of pipeComp; for the stable release version, see pipeComp.
pipeComp pipeline benchmarking framework
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>
citation("pipeComp")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("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")| 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 | 1.17.0 |
| 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_1.17.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |