Package: pipeFrame
Type: Package
Title: Pipeline framework for bioinformatics in R
Version: 1.28.0
Author: Zheng Wei, Shining Ma
Maintainer: Zheng Wei <wzweizheng@qq.com>
Description: 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.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0.0),
Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings,
        Seqinfo, parallel, stats, utils, rmarkdown
Suggests: BiocManager, knitr, rtracklayer, testthat,
        BSgenome.Hsapiens.UCSC.hg19
RoxygenNote: 7.0.2
VignetteBuilder: knitr
biocViews: Software, Infrastructure, WorkflowStep
URL: https://github.com/wzthu/pipeFrame
BugReports: https://github.com/wzthu/pipeFrame/issues
Config/pak/sysreqs: cmake make libbz2-dev liblzma-dev libuv1-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:50:08 UTC
RemoteUrl: https://github.com/bioc/pipeFrame
RemoteRef: RELEASE_3_23
RemoteSha: 7f135285e634b90c815cbaad2da871cc6f679783
NeedsCompilation: no
Packaged: 2026-04-29 23:51:11 UTC; root
Built: R 4.6.0; ; 2026-04-30 01:25:43 UTC; unix
