pipeFrame

DOI: 10.18129/B9.bioc.pipeFrame  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see pipeFrame.

Pipeline framework for bioinformatics in R

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	An Introduction to pipeFrame
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, Software, WorkflowStep
Version	1.16.0
In Bioconductor since	BioC 3.9 (R-3.6) (4.5 years)
License	GPL-3
Depends	R (>= 4.0.0)
Imports	BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils, rmarkdown
LinkingTo
Suggests	BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL	https://github.com/wzthu/pipeFrame
BugReports	https://github.com/wzthu/pipeFrame/issues
Depends On Me	enrichTF, esATAC
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	pipeFrame_1.16.0.tar.gz
Windows Binary	pipeFrame_1.16.0.zip (64-bit only)
macOS Binary (x86_64)	pipeFrame_1.16.0.tgz
macOS Binary (arm64)	pipeFrame_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pipeFrame
Source Repository (Developer Access)	git clone [email protected]:packages/pipeFrame
Bioc Package Browser	https://code.bioconductor.org/browse/pipeFrame/
Package Short Url	https://bioconductor.org/packages/pipeFrame/
Package Downloads Report	Download Stats