pipeComp
This is the development version of pipeComp; for the stable release version, see pipeComp.
pipeComp pipeline benchmarking framework
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.23.5 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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_1.23.5.tar.gz |
| Windows Binary (x86_64) | pipeComp_1.23.5.zip |
| macOS Binary (big-sur-x86_64) | pipeComp_1.23.5.tgz |
| macOS Binary (sonoma-arm64) | pipeComp_1.23.5.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 |