{
  "_id": "6a1af8401d7bb097a09fac66",
  "Package": "systemPipeR",
  "Type": "Package",
  "Title": "systemPipeR: A Multipurpose Workflow Management System for\nReproducible Data Analysis",
  "Version": "2.19.0",
  "Date": "2026-03-05",
  "Author": "Thomas Girke",
  "Maintainer": "Thomas Girke <thomas.girke@ucr.edu>",
  "biocViews": "Genetics, Infrastructure, DataImport, Sequencing, RNASeq,\nRiboSeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage,\nGeneSetEnrichment, Alignment, QualityControl, ImmunoOncology,\nReportWriting, WorkflowStep, WorkflowManagement",
  "Description": "systemPipeR is a workflow management environment for\nreproducible data analysis that integrates R with command-line\nsoftware. It enables researchers to design, execute, and report\ncomplex workflows on local machines and HPC systems. The\nframework combines R-based analysis with external tools through\na Common Workflow Language (CWL) interface, manages workflow\ndependencies and restart capabilities, and automatically\ngenerates reproducible scientific analysis reports. The\ncompanion package systemPipeRdata provides ready-to-use\nworkflow templates that simplify workflow setup and\ncustomization. Alternatively, workflow templates can be loaded\nfrom dedicated GitHub repositories.",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "systemPipeR can be used to run external\ncommand-line software (e.g. short read aligners), but the\ncorresponding tool needs to be installed on a system.",
  "License": "Artistic-2.0",
  "URL": "https://github.com/tgirke/systemPipeR",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:39:44 UTC",
  "RemoteUrl": "https://github.com/bioc/systemPipeR",
  "RemoteRef": "HEAD",
  "RemoteSha": "d92e8e37d25e39c013db2e37e4762411f66be9a0",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:47:14 UTC",
    "User": "root"
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  "_created": "2026-05-30T09:47:14.000Z",
  "_published": "2026-05-30T14:46:24.684Z",
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    "infrastructure",
    "dataimport",
    "sequencing",
    "rnaseq",
    "riboseq",
    "chipseq",
    "methylseq",
    "snp",
    "geneexpression",
    "coverage",
    "genesetenrichment",
    "alignment",
    "qualitycontrol",
    "immunooncology",
    "reportwriting",
    "workflowstep",
    "workflowmanagement"
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "source": "https://www.bioconductor.org/packages/stats/bioc/systemPipeR"
  },
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  "_devurl": "https://github.com/tgirke/systempiper",
  "_searchresults": 488,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/systemPipeR.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/tgirke/systempiper",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addResources",
    "alignStats",
    "appendCodeLine<-",
    "appendParam",
    "appendParam2",
    "appendStep<-",
    "as.list",
    "baseCommand",
    "catlist",
    "catmap",
    "check.outfiles",
    "check.output",
    "clt",
    "clusterRun",
    "cmdlist",
    "cmdToCwl",
    "cmdToCwl<-",
    "codeChunkStart",
    "codeLine",
    "combineVarReports",
    "complexitylevels",
    "config.param",
    "configWF",
    "copyEnvir",
    "cores",
    "countRangeset",
    "createParam",
    "createParamFiles",
    "cwlFilesUpdate",
    "dependency",
    "dependency<-",
    "evalCode",
    "featureCoverage",
    "featuretypeCounts",
    "files",
    "filterDEGs",
    "filterVars",
    "genFeatures",
    "getColumn",
    "goBarplot",
    "GOCluster_Report",
    "GOHyperGAll",
    "GOHyperGAll_Simplify",
    "GOHyperGAll_Subset",
    "idconv",
    "importWF",
    "infile1",
    "infile2",
    "input",
    "inputvars",
    "intersectlist",
    "intersectmatrix",
    "linewise",
    "LineWise",
    "listCmdModules",
    "listCmdTools",
    "loadWF",
    "loadWorkflow",
    "makeCATdb",
    "mergeBamByFactor",
    "module",
    "moduleAvail",
    "moduleClear",
    "moduleInit",
    "modulelist",
    "moduleload",
    "modules",
    "moduleUnload",
    "olBarplot",
    "olRanges",
    "other",
    "outfile1",
    "outfiles",
    "outpaths",
    "output",
    "output_update",
    "overLapper",
    "plotfeatureCoverage",
    "plotfeaturetypeCounts",
    "plotWF",
    "plotwfOutput",
    "predORF",
    "preprocessReads",
    "printParam",
    "printParam2",
    "projectInfo",
    "readComp",
    "reference",
    "removeParam2",
    "renameParam",
    "renameParam2",
    "renameStep<-",
    "renderLogs",
    "renderPlotwf",
    "renderReport",
    "renderWF",
    "replaceCodeLine<-",
    "replaceParam",
    "replaceParam2",
    "replaceStep<-",
    "results",
    "returnRPKM",
    "rmdPath",
    "run_DESeq2",
    "run_edgeR",
    "runCommandline",
    "runDiff",
    "runInfo",
    "runWF",
    "sal2bash",
    "sal2rmd",
    "SampleName",
    "scaleRanges",
    "SE",
    "SE<-",
    "seeFastq",
    "seeFastqPlot",
    "setlist",
    "show",
    "showDF",
    "software",
    "SPRproject",
    "status",
    "statusWF",
    "stepName",
    "stepsWF",
    "subset",
    "subsetParam",
    "subsetWF",
    "symLink2bam",
    "sysargs",
    "sysargs2",
    "sysargslist",
    "SYSargsList",
    "systemArgs",
    "targets",
    "targets.as.df",
    "targets.as.list",
    "targetsheader",
    "targetsin",
    "targetsout",
    "targetsWF",
    "trimbatch",
    "tryCL",
    "tryCMD",
    "tryPath",
    "updateColumn<-",
    "updateWF",
    "variantReport",
    "varSummary",
    "vennlist",
    "vennPlot",
    "viewEnvir",
    "wf",
    "write_SYSargsList",
    "writeParamFiles",
    "writeTargets",
    "writeTargetsout",
    "writeTargetsRef",
    "yamlinput",
    "yamlinput<-"
  ],
  "_help": [
    {
      "page": "systemPipeR-package",
      "title": "systemPipeR package for Workflow Environment",
      "topics": [
        "systemPipeR-package"
      ]
    },
    {
      "page": "add-methods",
      "title": "Extension accessor methods for SummarizedExperiment object",
      "topics": [
        "addAssay",
        "addAssay,SummarizedExperiment-method",
        "addAssay-methods",
        "addMetadata",
        "addMetadata,SummarizedExperiment-method",
        "addMetadata-methods"
      ]
    },
    {
      "page": "alignStats",
      "title": "Alignment statistics",
      "topics": [
        "alignStats"
      ]
    },
    {
      "page": "catDB-class",
      "title": "Class '\"catDB\"'",
      "topics": [
        "catDB-class",
        "catlist,catDB-method",
        "catmap,catDB-method",
        "coerce,list,catDB-method",
        "idconv,catDB-method",
        "names,catDB-method",
        "show,catDB-method"
      ]
    },
    {
      "page": "catmap",
      "title": "catDB accessor methods",
      "topics": [
        "catlist",
        "catlist-methods",
        "catmap",
        "catmap-methods",
        "idconv",
        "idconv-methods"
      ]
    },
    {
      "page": "check.output",
      "title": "Checking if the outfiles files exist",
      "topics": [
        "check.outfiles",
        "check.output"
      ]
    },
    {
      "page": "clusterRun",
      "title": "Submit command-line tools to cluster",
      "topics": [
        "clusterRun"
      ]
    },
    {
      "page": "config.param",
      "title": "Adding param file",
      "topics": [
        "config.param"
      ]
    },
    {
      "page": "configWF",
      "title": "Workflow Steps Selection",
      "topics": [
        "configWF"
      ]
    },
    {
      "page": "countRangeset",
      "title": "Read counting for several range sets",
      "topics": [
        "countRangeset"
      ]
    },
    {
      "page": "createParamFiles",
      "title": "createParam",
      "topics": [
        "createParam",
        "createParamFiles",
        "writeParamFiles"
      ]
    },
    {
      "page": "cwlFilesUpdate",
      "title": "Update CWL description files",
      "topics": [
        "cwlFilesUpdate"
      ]
    },
    {
      "page": "EnvModules-class",
      "title": "Class '\"EnvModules\"'",
      "topics": [
        "$,EnvModules-method",
        "available_modules,EnvModules-method",
        "coerce,EnvModules,list-method",
        "coerce,list,EnvModules-method",
        "default_modules,EnvModules-method",
        "EnvModules,EnvModules-method",
        "EnvModules-class",
        "loaded_modules,EnvModules-method",
        "modulecmd,EnvModules-method",
        "names,EnvModules-method",
        "show,EnvModules-method",
        "[,EnvModules,ANY,ANY,ANY-method",
        "[[,EnvModules,ANY,ANY-method",
        "[[,EnvModules,ANY,missing-method",
        "[[<-,EnvModules,ANY,ANY,ANY-method",
        "[[<-,EnvModules,ANY,ANY-method",
        "[[<-,EnvModules-method"
      ]
    },
    {
      "page": "evalCode",
      "title": "Toggles option 'eval' on the RMarkdown files",
      "topics": [
        "evalCode"
      ]
    },
    {
      "page": "featureCoverage",
      "title": "Genome read coverage by transcript models",
      "topics": [
        "featureCoverage"
      ]
    },
    {
      "page": "featuretypeCounts",
      "title": "Plot read distribution across genomic features",
      "topics": [
        "featuretypeCounts"
      ]
    },
    {
      "page": "filterDEGs",
      "title": "Filter and plot DEG results",
      "topics": [
        "filterDEGs"
      ]
    },
    {
      "page": "filterVars",
      "title": "Filter VCF files",
      "topics": [
        "filterVars"
      ]
    },
    {
      "page": "genFeatures",
      "title": "Generate feature ranges from TxDb",
      "topics": [
        "genFeatures"
      ]
    },
    {
      "page": "GOHyperGAll",
      "title": "GO term enrichment analysis for large numbers of gene sets",
      "topics": [
        "goBarplot",
        "GOCluster_Report",
        "GOHyperGAll",
        "GOHyperGAll_Simplify",
        "GOHyperGAll_Subset",
        "makeCATdb"
      ]
    },
    {
      "page": "importWF",
      "title": "Import R Markdown file as workflow",
      "topics": [
        "importWF"
      ]
    },
    {
      "page": "INTERSECTset-class",
      "title": "Class '\"INTERSECTset\"'",
      "topics": [
        "as.list,INTERSECTset-method",
        "coerce,list,INTERSECTset-method",
        "complexitylevels,INTERSECTset-method",
        "intersectlist,INTERSECTset-method",
        "intersectmatrix,INTERSECTset-method",
        "INTERSECTset-class",
        "length,INTERSECTset-method",
        "names,INTERSECTset-method",
        "setlist,INTERSECTset-method",
        "show,INTERSECTset-method"
      ]
    },
    {
      "page": "LineWise-class",
      "title": "Class '\"LineWise\"'",
      "topics": [
        "$,LineWise-method",
        "appendCodeLine,LineWise-method",
        "appendCodeLine<-,LineWise-method",
        "codeChunkStart",
        "codeChunkStart,LineWise-method",
        "codeLine,LineWise-method",
        "coerce,LineWise,list-method",
        "coerce,list,LineWise-method",
        "dependency,LineWise-method",
        "files,LineWise-method",
        "length,LineWise-method",
        "LineWise",
        "linewise",
        "linewise,LineWise-method",
        "LineWise-class",
        "names,LineWise-method",
        "replaceCodeLine,LineWise-method",
        "replaceCodeLine<-,LineWise-method",
        "rmdPath",
        "rmdPath,LineWise-method",
        "runInfo,LineWise-method",
        "show,LineWise-method",
        "status,LineWise-method",
        "stepName,LineWise-method",
        "[,LineWise,ANY,ANY,ANY-method",
        "[[,LineWise,ANY,missing-method",
        "[[<-,LineWise,ANY,ANY,ANY-method",
        "[[<-,LineWise,ANY,ANY-method"
      ]
    },
    {
      "page": "listCmdTools",
      "title": "List/check the existence of command-line tools of a workflow",
      "topics": [
        "listCmdModules",
        "listCmdTools"
      ]
    },
    {
      "page": "loadWorkflow",
      "title": "Constructs SYSargs2 object from CWL param and targets files",
      "topics": [
        "loadWF",
        "loadWorkflow",
        "renderWF",
        "updateWF"
      ]
    },
    {
      "page": "mergeBamByFactor",
      "title": "Merge BAM files based on factor",
      "topics": [
        "mergeBamByFactor"
      ]
    },
    {
      "page": "moduleload",
      "title": "Interface to allow full use of the Environment Modules system for Unix",
      "topics": [
        "module",
        "moduleAvail",
        "moduleClear",
        "moduleInit",
        "modulelist",
        "moduleload",
        "moduleUnload"
      ]
    },
    {
      "page": "olBarplot",
      "title": "Bar plot for intersect sets",
      "topics": [
        "olBarplot"
      ]
    },
    {
      "page": "olRanges",
      "title": "Identify Range Overlaps for IRanges and GRanges Object",
      "topics": [
        "olRanges"
      ]
    },
    {
      "page": "output_update",
      "title": "Updates the output files paths in the 'SYSargs2' object",
      "topics": [
        "output_update"
      ]
    },
    {
      "page": "overLapper",
      "title": "Set Intersect and Venn Diagram Functions",
      "topics": [
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        "complexitylevels-methods",
        "intersectlist",
        "intersectlist-methods",
        "intersectmatrix",
        "intersectmatrix-methods",
        "overLapper",
        "setlist",
        "setlist-methods",
        "vennlist",
        "vennlist-methods"
      ]
    },
    {
      "page": "plotfeatureCoverage",
      "title": "Plot feature coverage results",
      "topics": [
        "plotfeatureCoverage"
      ]
    },
    {
      "page": "plotfeaturetypeCounts",
      "title": "Plot read distribution across genomic features",
      "topics": [
        "plotfeaturetypeCounts"
      ]
    },
    {
      "page": "plotWF",
      "title": "Visualize SPR workflow and status",
      "topics": [
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        "plotwfOutput",
        "renderPlotwf"
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    {
      "page": "predORF",
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        "predORF"
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      "page": "preprocessReads",
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      "page": "ParamFiles",
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        "printParam",
        "renameParam",
        "replaceParam",
        "subsetParam"
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      "page": "ParamFiles2",
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        "printParam2",
        "removeParam2",
        "renameParam2",
        "replaceParam2"
      ]
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      "page": "readComp",
      "title": "Import sample comparisons from targets file",
      "topics": [
        "readComp"
      ]
    },
    {
      "page": "renderLogs",
      "title": "Render RMarkdown Logs Report",
      "topics": [
        "renderLogs"
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    {
      "page": "renderReport",
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        "renderReport"
      ]
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    {
      "page": "returnRPKM",
      "title": "RPKM Normalization",
      "topics": [
        "returnRPKM"
      ]
    },
    {
      "page": "run_DESeq2",
      "title": "Runs DESeq2",
      "topics": [
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      ]
    },
    {
      "page": "run_edgeR",
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      "topics": [
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    {
      "page": "runCommandline",
      "title": "Execute SYSargs and SYSargs2",
      "topics": [
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      ]
    },
    {
      "page": "runDiff",
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      ]
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    {
      "page": "runWF",
      "title": "Execute SYSargsList",
      "topics": [
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      "page": "sal2bash",
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      "page": "sal2rmd",
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      "page": "scaleRanges",
      "title": "Scale spliced ranges to genome coordinates",
      "topics": [
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    },
    {
      "page": "seeFastq",
      "title": "Quality reports for FASTQ files",
      "topics": [
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        "seeFastqPlot"
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    },
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      "page": "showDF",
      "title": "Create an HTML table using DT package with fixed columns",
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        "showDF"
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    },
    {
      "page": "SPRproject",
      "title": "Workflow Project Initiation",
      "topics": [
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      "page": "subsetWF",
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      "page": "symLink2bam",
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      "page": "targets.as.df",
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      "page": "trimbatch",
      "title": "Genome read coverage by transcript models",
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    {
      "page": "tryCMD",
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      "topics": [
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      "page": "tryPath",
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      "page": "variantReport",
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      "topics": [
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      "page": "vennPlot",
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      "page": "write_SYSargsList",
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      "page": "writeTargets",
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      "page": "writeTargetsout",
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      "page": "writeTargetsRef",
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      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676683274"
    }
  ]
}