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

Pipeline framework for bioinformatics in R

Bioconductor version: Development (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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

An Introduction to pipeFrame HTML R Script
Reference Manual PDF


biocViews Infrastructure, Software, WorkflowStep
Version 1.21.0
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
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Suggests BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19
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Follow Installation instructions to use this package in your R session.

Source Package pipeFrame_1.21.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) pipeFrame_1.21.0.tgz
macOS Binary (arm64) pipeFrame_1.21.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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