pipeFrame

This is the development version of pipeFrame; for the stable release version, see pipeFrame.

Pipeline framework for bioinformatics in R

Bioconductor version: Development (3.21)

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 (from within R, enter citation("pipeFrame")):

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("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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, Software, WorkflowStep
Version	1.21.0
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

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_1.21.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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