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pipeFrame

Pipeline framework for bioinformatics in R


Bioconductor version: Release (3.18)

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 "4.3") 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")
An Introduction to pipeFrame HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Infrastructure, Software, WorkflowStep
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (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 enrichTF, 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_1.18.0.tar.gz
Windows Binary pipeFrame_1.18.0.zip
macOS Binary (x86_64) pipeFrame_1.18.0.tgz
macOS Binary (arm64) pipeFrame_1.18.0.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