pipeFrame
Pipeline framework for bioinformatics in R
Bioconductor version: Release (3.20)
pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.
Author: Zheng Wei, Shining Ma
Maintainer: Zheng Wei <wzweizheng at qq.com>
citation("pipeFrame")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pipeFrame")
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("pipeFrame")| An Introduction to pipeFrame | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, Software, WorkflowStep |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0.0) |
| Imports | BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils, rmarkdown |
| System Requirements | |
| URL | https://github.com/wzthu/pipeFrame |
| Bug Reports | https://github.com/wzthu/pipeFrame/issues |
See More
| Suggests | BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 |
| Linking To | |
| Enhances | |
| Depends On Me | esATAC |
| 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 | pipeFrame_1.22.0.tar.gz |
| Windows Binary (x86_64) | pipeFrame_1.22.0.zip (64-bit only) |
| macOS Binary (x86_64) | pipeFrame_1.22.0.tgz |
| macOS Binary (arm64) | pipeFrame_1.21.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pipeFrame |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pipeFrame |
| Bioc Package Browser | https://code.bioconductor.org/browse/pipeFrame/ |
| Package Short Url | https://bioconductor.org/packages/pipeFrame/ |
| Package Downloads Report | Download Stats |