{
  "_id": "6aca1ebdfe5cc25786e84e31",
  "Package": "systemPipeRdata",
  "Title": "systemPipeRdata: Workflow templates and sample data",
  "Version": "2.16.0",
  "Date": "2026-03-05",
  "Author": "Thomas Girke",
  "Maintainer": "Thomas Girke <thomas.girke@ucr.edu>",
  "Encoding": "UTF-8",
  "biocViews": "Genetics, Infrastructure, DataImport, Sequencing, RNASeq,\nChIPSeq, MethylSeq, SNP, GeneExpression, Coverage,\nGeneSetEnrichment, Alignment, QualityControl, ImmunoOncology,\nRiboSeq, WorkflowStep",
  "Description": "systemPipeRdata complements the systemPipeR workflow\nmanagement system (WMS) by offering a collection of\npre-designed data analysis workflow templates. These templates\nare easily accessible and can be readily loaded onto a user's\nsystem with a single command. Once loaded, the WMS can\nimmediately utilize these templates for efficient end-to-end\nanalysis, serving a wide range of data analysis needs.",
  "VignetteBuilder": "knitr",
  "License": "Artistic-2.0",
  "NeedsCompilation": "no",
  "URL": "https://github.com/tgirke/systemPipeRdata",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "git zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:28:35 UTC",
  "RemoteUrl": "https://github.com/bioc/systemPipeRdata",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "870c05955c74be83bab68b13df17661c6ac88f9f",
  "Packaged": {
    "Date": "2026-10-10 11:09:23 UTC",
    "User": "root"
  },
  "_user": "bioc-release",
  "_type": "src",
  "_file": "systemPipeRdata_2.16.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/160c627523dc62d6805b7d73dab5900b2e6df19b22150dceef778916fc425b8b",
  "_filesize": 288720156,
  "_sha256": "160c627523dc62d6805b7d73dab5900b2e6df19b22150dceef778916fc425b8b",
  "_expires": "2027-01-18T11:17:06.000Z",
  "_created": "2026-10-10T11:09:23.000Z",
  "_published": "2026-10-10T11:17:16.913Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047137431",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 3,
    "warning": 2,
    "note": 16
  },
  "_upstream": "https://github.com/bioc/systemPipeRdata",
  "_commit": {
    "id": "870c05955c74be83bab68b13df17661c6ac88f9f",
    "author": "lshep <lori.shepherd@roswellpark.org>",
    "committer": "lshep <lori.shepherd@roswellpark.org>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379315
  },
  "_maintainer": {
    "name": "Thomas Girke",
    "email": "thomas.girke@ucr.edu",
    "login": "tgirke",
    "description": "",
    "uuid": 1336916
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114199838499,
      "time": 196,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11668286919"
    },
    {
      "job": 114199838548,
      "time": 317,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11668142367"
    },
    {
      "job": 114199838532,
      "time": 307,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11668381975"
    },
    {
      "job": 114198888445,
      "time": 335,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11668690473"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "remotes",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Suggests"
    },
    {
      "package": "DT",
      "role": "Suggests"
    },
    {
      "package": "txdbmaker",
      "role": "Suggests"
    },
    {
      "package": "GenomicRanges",
      "role": "Suggests"
    },
    {
      "package": "IRanges",
      "role": "Suggests"
    },
    {
      "package": "Rsamtools",
      "role": "Suggests"
    },
    {
      "package": "ShortRead",
      "role": "Suggests"
    },
    {
      "package": "rtracklayer",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "systemPipeR",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    },
    {
      "package": "magrittr",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "gert",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-01",
      "n": 4
    },
    {
      "week": "2026-02",
      "n": 4
    },
    {
      "week": "2026-03",
      "n": 1
    },
    {
      "week": "2026-04",
      "n": 3
    },
    {
      "week": "2026-08",
      "n": 5
    },
    {
      "week": "2026-10",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.17.1",
      "bioc": "3.24",
      "repository": "data/experiment"
    },
    {
      "branch": "release",
      "version": "2.16.0",
      "bioc": "3.23",
      "repository": "data/experiment"
    }
  ],
  "_topics": [
    "genetics",
    "infrastructure",
    "dataimport",
    "sequencing",
    "rnaseq",
    "chipseq",
    "methylseq",
    "snp",
    "geneexpression",
    "coverage",
    "genesetenrichment",
    "alignment",
    "qualitycontrol",
    "immunooncology",
    "riboseq",
    "workflowstep",
    "datapkg"
  ],
  "_stars": 9,
  "_contributors": [
    {
      "user": "dcassol",
      "count": 216,
      "uuid": 12722576
    },
    {
      "user": "tgirke",
      "count": 65,
      "uuid": 1336916
    },
    {
      "user": "lz100",
      "count": 50,
      "uuid": 35240440
    },
    {
      "user": "hpages",
      "count": 18,
      "uuid": 8810451
    },
    {
      "user": "lshep",
      "count": 8,
      "uuid": 18724380
    },
    {
      "user": "dtenenba",
      "count": 6,
      "uuid": 2286826
    },
    {
      "user": "nturaga",
      "count": 5,
      "uuid": 2746443
    },
    {
      "user": "gh-action-bot",
      "count": 4,
      "uuid": 76133068
    },
    {
      "user": "jwokaty",
      "count": 4,
      "uuid": 1744257
    },
    {
      "user": "imgbotapp",
      "count": 1,
      "uuid": 31427850
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/tgirke/systempiperdata",
  "_searchresults": 169,
  "_datapkg": true,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/systemPipeRdata.html"
  ],
  "_cranurl": false,
  "_exports": [
    "availableWF",
    "genWorkenvir",
    "genWorkenvir_gh",
    "getData_gh",
    "getParam_gh",
    "getSubsetReads",
    "pathList"
  ],
  "_help": [
    {
      "page": "availableWF",
      "title": "List Available Workflows Templates at 'systemPipeRdata' package",
      "topics": [
        "availableWF"
      ]
    },
    {
      "page": "genWorkenvir",
      "title": "Generate workflow templates",
      "topics": [
        "genWorkenvir"
      ]
    },
    {
      "page": "genWorkenvir_gh",
      "title": "Clone a workflow repository using gert and enforce version requirements",
      "topics": [
        "genWorkenvir_gh"
      ]
    },
    {
      "page": "getData_gh",
      "title": "Install a shared workflow data directory from a GitHub tag archive",
      "topics": [
        "getData_gh"
      ]
    },
    {
      "page": "getParam_gh",
      "title": "Install a shared CWL parameter directory from a GitHub tag archive",
      "topics": [
        "getParam_gh"
      ]
    },
    {
      "page": "getSubsetReads",
      "title": "Subsetting fastq data",
      "topics": [
        "getSubsetReads"
      ]
    },
    {
      "page": "pathList",
      "title": "Return location of sample data",
      "topics": [
        "pathList"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/systemPipeRdata/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "BiocGenerics",
    "Biostrings",
    "crayon",
    "generics",
    "IRanges",
    "jsonlite",
    "remotes",
    "S4Vectors",
    "Seqinfo",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "systemPipeRdata.Rmd",
      "filename": "systemPipeRdata.html",
      "title": "systemPipeRdata: Workflow templates and sample data",
      "author": "Author: Le Zhang, Daniela Cassol, and Thomas Girke",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting started",
        "Installation",
        "Loading package and documentation",
        "Overview of workflow templates",
        "Use workflow templates",
        "Load a workflow",
        "Run and visualize workflow",
        "Additional workflow templates on GitHub",
        "Useful functionalities",
        "Create workflow templates interactively",
        "Return paths to sample data",
        "Analysis steps in selected workflows",
        "Generic template",
        "RNA-Seq workflow",
        "ChIP-Seq Workflow",
        "VAR-Seq Workflow",
        "Ribo-Seq Workflow",
        "scRNA-Seq Workflow",
        "BLAST Workflow",
        "Cheminformatics Workflow",
        "Version information",
        "Funding",
        "References"
      ],
      "created": "2015-09-15 16:11:46",
      "modified": "2026-03-06 04:07:27",
      "commits": 32
    },
    {
      "source": "new.Rmd",
      "filename": "new.html",
      "title": "Generic Workflow Template",
      "author": "Author: FirstName LastName",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Workflow environment",
        "Create workflow environment",
        "Construct workflow",
        "Step 1: Load packages",
        "Step 2: Export tabular data to files",
        "Step 3: Compress data",
        "Step 4: Uncompress data",
        "Step 5: Import tabular files and visualize data",
        "Version Information",
        "Automated routine",
        "CL tools used",
        "Session Info",
        "References"
      ],
      "created": "2024-08-03 23:15:22",
      "modified": "2024-10-07 00:05:11",
      "commits": 8
    },
    {
      "source": "SPscrna.Rmd",
      "filename": "SPscrna.html",
      "title": "Single Cell RNAseq",
      "author": "Author: FirstName LastName",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overview",
        "Experimental design",
        "Workflow steps",
        "Load workflow environment",
        "Input data: targets file",
        "Quick start",
        "Load packages",
        "Load data",
        "Simple count visulization",
        "Create Seurat object",
        "QC of cells",
        "Filter cells",
        "Normalization",
        "Find highly variable genes",
        "Scaling",
        "PCA",
        "Plot PCA results",
        "Find optimal PCs",
        "Clustering",
        "Visualize clusters with UMAP/tSNE",
        "Find cluster biomarkers",
        "Visualize markers",
        "Classify cell types",
        "Workflow session",
        "Manage the workflow",
        "About the workflow",
        "Tools used",
        "Session Info"
      ],
      "created": "2023-08-21 22:00:32",
      "modified": "2024-10-16 23:42:28",
      "commits": 4
    },
    {
      "source": "SPblast.Rmd",
      "filename": "SPblast.html",
      "title": "BLAST Workflow Template",
      "author": "Author: FirstName LastName",
      "engine": "knitr::rmarkdown",
      "headings": [
        "About this template",
        "Workflow environment",
        "Step 1: Load packages",
        "Step 2: Test BLAST install",
        "Step 3: BLASTable database",
        "Step 4: BLAST search",
        "Step 5: View top hits",
        "Version Information",
        "Automated routine",
        "CL tools used",
        "Session Info"
      ],
      "created": "2023-08-21 22:00:32",
      "modified": "2024-10-07 00:05:11",
      "commits": 7
    },
    {
      "source": "SPcheminfo.Rmd",
      "filename": "SPcheminfo.html",
      "title": "Cheminformatics Drug Similarity Template",
      "author": "Author: FirstName LastName",
      "engine": "knitr::rmarkdown",
      "headings": [
        "About the template",
        "Workflow environment",
        "Step 1: Load packages",
        "Step 2: Import molecule structures",
        "Step 3: Visualize molecule structures",
        "Step 4: Physicochemical properties",
        "Step 5: Box plots of properties",
        "Step 6: Structural descriptors",
        "Step 7: Removal of identical fingerprint sets",
        "Step 8: Similarity compute",
        "Step 9: Hierarchical clustering",
        "Step 10: PCA",
        "Step 11: Include heatmap",
        "Version information",
        "Automated routine",
        "CL tools used",
        "Session Info"
      ],
      "created": "2023-08-21 22:00:32",
      "modified": "2024-10-07 00:05:11",
      "commits": 4
    },
    {
      "source": "systemPipeChIPseq.Rmd",
      "filename": "systemPipeChIPseq.html",
      "title": "ChIP-Seq Workflow Template",
      "author": "Author: First Last Name",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overview",
        "Experimental design",
        "Workflow steps",
        "Load workflow environment",
        "Input data: targets file",
        "Quick start",
        "Load packages",
        "Read preprocessing",
        "FASTQ quality report",
        "Preprocessing with preprocessReads function",
        "Alignments",
        "Read mapping with Bowtie2",
        "Read and alignment stats",
        "Create symbolic links for viewing BAM files in IGV",
        "Utilities for coverage data",
        "Rle object stores coverage information",
        "Resizing aligned reads",
        "Naive peak calling",
        "Plot coverage for defined region",
        "Peak calling with MACS2",
        "Merge BAM files of replicates prior to peak calling",
        "Peak calling without input/reference sample",
        "Peak calling with input/reference sample",
        "Identify consensus peaks",
        "Annotate peaks with genomic context",
        "Annotation with ChIPseeker package",
        "Annotation with ChIPpeakAnno package",
        "Count reads overlapping peaks",
        "Differential binding analysis",
        "GO term enrichment analysis",
        "Motif analysis",
        "Parse DNA sequences of peak regions from genome",
        "Motif discovery with BCRANK",
        "Version Information",
        "Running workflow",
        "Interactive job submissions in a single machine",
        "Parallelization on clusters",
        "Visualize workflow",
        "Checking workflow status",
        "Accessing logs report",
        "Tools used",
        "Session Info",
        "Funding",
        "References"
      ],
      "created": "2019-04-16 22:38:35",
      "modified": "2024-10-07 00:05:11",
      "commits": 17
    },
    {
      "source": "systemPipeRIBOseq.Rmd",
      "filename": "systemPipeRIBOseq.html",
      "title": "RIBO-Seq Workflow Template",
      "author": "Author: First Last Name",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Experimental design",
        "Workflow environment",
        "Load packages and sample data",
        "Generate workflow environment",
        "Experiment definition provided by targets file",
        "Required packages and resources",
        "Read preprocessing",
        "Preprocessing with preprocessReads function",
        "FASTQ quality report",
        "Alignments",
        "Read mapping with HISAT2",
        "HISAT2 mapping",
        "Read and alignment stats",
        "Create symbolic links for viewing BAM files in IGV",
        "Read distribution across genomic features",
        "Obtain feature types",
        "Count and plot reads of any length",
        "Count and plot reads of specific lengths",
        "Adding custom features to workflow",
        "Predicting uORFs in 5' UTR regions",
        "Adding custom features to other feature types",
        "Predicting sORFs in intergenic regions",
        "Genomic read coverage along transripts or CDSs",
        "Binned CDS coverage to compare many transcripts",
        "Coverage upstream and downstream of start and stop codons",
        "Combined coverage for both binned CDS and start/stop codons",
        "Nucleotide level coverage along entire transcripts/CDSs",
        "Read quantification per annotation range",
        "Read counting with summarizeOverlaps in parallel mode using multiple cores",
        "Sample-wise correlation analysis",
        "Analysis of differentially expressed genes with edgeR",
        "Plot DEG results",
        "Venn diagrams of DEG sets",
        "GO term enrichment analysis of DEGs",
        "Obtain gene-to-GO mappings",
        "Batch GO term enrichment analysis",
        "Plot batch GO term results",
        "Differential ribosome loading analysis (translational efficiency)",
        "Clustering and heat maps",
        "Version Information",
        "Running workflow",
        "Interactive job submissions in a single machine",
        "Parallelization on clusters",
        "Visualize workflow",
        "Checking workflow status",
        "Accessing logs report",
        "Tools used",
        "Report  Information",
        "Funding",
        "References"
      ],
      "created": "2019-04-16 22:38:35",
      "modified": "2024-08-03 23:15:22",
      "commits": 16
    },
    {
      "source": "systemPipeRNAseq.Rmd",
      "filename": "systemPipeRNAseq.html",
      "title": "RNA-Seq Workflow Template",
      "author": "Author: First Last Name",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overview",
        "Experimental design",
        "Workflow steps",
        "Load workflow environment",
        "Input data: targets file",
        "Quick start",
        "Load packages",
        "Read preprocessing",
        "With preprocessReads",
        "With Trimmomatic",
        "FASTQ quality report",
        "Short read alignments",
        "Read mapping with HISAT2",
        "HISAT2 mapping",
        "Alignment stats",
        "Viewing BAM files in IGV",
        "Read quantification",
        "Gene annotation database",
        "Read counting with summarizeOverlaps",
        "Sample-wise clustering",
        "Analysis of DEGs",
        "Run edgeR",
        "Add gene descriptions",
        "Plot DEG results",
        "Venn diagrams of DEG sets",
        "GO term enrichment analysis",
        "Obtain gene-to-GO mappings",
        "Batch GO term enrichment analysis",
        "Plot batch GO term results",
        "Clustering and heat maps",
        "Workflow session information",
        "Additional details",
        "Running workflows",
        "Parallelization on clusters",
        "CL tools used",
        "Session info",
        "Funding",
        "References"
      ],
      "created": "2019-04-16 22:38:35",
      "modified": "2026-01-21 01:45:25",
      "commits": 28
    },
    {
      "source": "systemPipeVARseq.Rmd",
      "filename": "systemPipeVARseq.html",
      "title": "VAR-Seq Workflow Template",
      "author": "Author: First Last Name",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overview",
        "Experimental design",
        "Workflow steps",
        "Load workflow environment",
        "Input data: targets file",
        "Quick start",
        "Required packages and resources",
        "FASTQ quality reports",
        "With FastQC",
        "With seeFastq",
        "Read preprocessing",
        "Read trimming with Trimmomatic",
        "Preprocessing with preprocessReads",
        "Read mapping with BWA-MEM",
        "Index and dictionary files",
        "Mapping reads with BWA-MEM",
        "Read and alignment stats",
        "Sym links for viewing BAM files in IGV",
        "Variant calling with GATK",
        "Step1: fastq to ubam",
        "Step2: Merge bam and ubam",
        "Step3: Sort bam files by genomic coordinates",
        "Step4: Mark duplicates",
        "Step5: Fixing tags",
        "Step6: HaplotypeCaller",
        "Step7: Import all gvcfs",
        "Step8: Joint genotyping (cohort calling)",
        "Step9: Hard filter (cohort) variants",
        "Step10: Extract variants per sample",
        "Inspect VCF files",
        "Import VCFs into R",
        "Filter variants in R",
        "Filter statistics",
        "Annotate variants",
        "Annotate variants with SnpEff",
        "Combine annotation results among samples",
        "Summary table of variants",
        "Plot raw variants table by consequence",
        "Plot variants stats",
        "Compare high-impact variants by group",
        "Venn diagram of variants",
        "Plot variants programmatically",
        "Non-Synonymous Variants",
        "Pathway Enrichment",
        "Drug-Target Analysis",
        "Version information",
        "Additional details",
        "Running workflows",
        "Parallelization on clusters",
        "Visualize workflow",
        "Checking workflow status",
        "Accessing logs report",
        "Tools used",
        "Report Session Info",
        "Funding",
        "References"
      ],
      "created": "2019-04-16 22:38:35",
      "modified": "2026-01-20 00:32:10",
      "commits": 21
    }
  ],
  "_score": 8.634682277281923,
  "_indexed": false,
  "_nocasepkg": "systempiperdata",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/systemPipeRdata",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.16.0",
      "date": "2026-10-10T11:14:21.000Z",
      "distro": "resolute",
      "commit": "870c05955c74be83bab68b13df17661c6ac88f9f",
      "fileid": "https://r2.ropensci.org/1de014f8a69d880f5bb486c825f87a15aa2c6afcb48ccab125e9d4f807e18015",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047137431"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.16.0",
      "date": "2026-10-10T11:14:41.000Z",
      "distro": "resolute",
      "commit": "870c05955c74be83bab68b13df17661c6ac88f9f",
      "fileid": "https://r2.ropensci.org/e6893fe4d9ee0ced3fbad05ab34af29bef1f9a7fa14a7a356dcf8506e79aeb36",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047137431"
    }
  ]
}