Package: systemPipeR
Type: Package
Title: systemPipeR: A Multipurpose Workflow Management System for
        Reproducible Data Analysis
Version: 2.17.2
Date: 2026-03-05
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke@ucr.edu>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
        RiboSeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage,
        GeneSetEnrichment, Alignment, QualityControl, ImmunoOncology,
        ReportWriting, WorkflowStep, WorkflowManagement
Description: systemPipeR is a workflow management environment for reproducible data analysis that integrates R with command-line software. It enables researchers to design, execute, and report complex workflows on local machines and HPC systems. The framework combines R-based analysis with external tools through a Common Workflow Language (CWL) interface, manages workflow dependencies and restart capabilities, and automatically generates reproducible scientific analysis reports. The companion package systemPipeRdata provides ready-to-use workflow templates that simplify workflow setup and customization. Alternatively, workflow templates can be loaded from dedicated GitHub repositories. 
Depends: R (>= 4.1.0), Rsamtools (>= 1.31.2), Biostrings, ShortRead (>=
        1.37.1), methods
Imports: GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr,
        magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets
Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata,
        GenomicAlignments, grid, dplyr, testthat, rjson, annotate,
        AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT,
        rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools,
        GenomicFeatures, txdbmaker, GenomeInfoDbData, VariantAnnotation
        (>= 1.25.11)
VignetteBuilder: knitr
SystemRequirements: systemPipeR can be used to run external
        command-line software (e.g. short read aligners), but the
        corresponding tool needs to be installed on a system.
License: Artistic-2.0
URL: https://github.com/tgirke/systemPipeR
git_url: https://git.bioconductor.org/packages/systemPipeR
git_branch: devel
git_last_commit: e354aff
git_last_commit_date: 2026-03-05
Repository: Bioconductor 3.24
Date/Publication: 2026-04-20
NeedsCompilation: no
Packaged: 2026-04-21 01:10:33 UTC; biocbuild
