Package: pipeFrame
Type: Package
Title: Pipeline framework for bioinformatics in R
Version: 1.25.1
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
git_url: https://git.bioconductor.org/packages/pipeFrame
git_branch: devel
git_last_commit: e038682
git_last_commit_date: 2025-07-23
Repository: Bioconductor 3.22
Date/Publication: 2025-07-24
NeedsCompilation: no
Packaged: 2025-07-25 01:26:15 UTC; biocbuild
Built: R 4.5.1; ; 2025-07-25 13:56:28 UTC; windows
