{ "_id": "6a1c0d681d7bb097a0a2db01", "Package": "PICB", "Title": "piRNA Cluster Builder", "Version": "1.5.0", "Authors@R": "c(person(\"Pavol\", \"Genzor\", role = c(\"aut\")),\nperson(\"Aleksandr\", \"Friman\", email=\"haase-lab-bioinfo@nih.gov\", role = c(\"aut\")),\nperson(\"Daniel\", \"Stoyko\", role = c(\"aut\")),\nperson(\"Parthena\", \"Konstantinidou\", email=\"haase-lab-bioinfo@nih.gov\", role = c(\"aut\")),\nperson(\"Franziska\", \"Ahrend\", email=\"haase-lab-bioinfo@nih.gov\", role = c(\"aut\", \"cre\"), comment=c(ORCID = \"0009-0004-7464-3444\")),\nperson(\"Zuzana\", \"Loubalova\", email=\"haase-lab-bioinfo@nih.gov\", role = c(\"aut\")),\nperson(\"Yuejun\", \"Wang\", email=\"haase-lab-bioinfo@nih.gov\", role = c(\"aut\")),\nperson(\"Hernan\", \"Lorenzi\", email=\"haase-lab-bioinfo@nih.gov\", role = c(\"aut\")),\nperson(\"Astrid D\", \"Haase\", email=\"haase-lab-bioinfo@nih.gov\", role = c(\"aut\")))", "Description": "piRNAs (short for PIWI-interacting RNAs) and their PIWI\nprotein partners play a key role in fertility and maintaining\ngenome integrity by restricting mobile genetic elements\n(transposons) in germ cells. piRNAs originate from genomic\nregions known as piRNA clusters. The piRNA Cluster Builder\n(PICB) is a versatile toolkit designed to identify genomic\nregions with a high density of piRNAs. It constructs piRNA\nclusters through a stepwise integration of unique and\nmultimapping piRNAs and offers wide-ranging parameter settings,\nsupported by an optimization function that allows users to test\ndifferent parameter combinations to tailor the analysis to\ntheir specific piRNA system. The output includes extensive\nmetadata columns, enabling researchers to rank clusters and\nextract cluster characteristics.", "License": "CC0", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "BugReports": "https://github.com/HaaseLab/PICB/issues", "URL": "https://github.com/HaaseLab/PICB", "biocViews": "Genetics, GenomeAnnotation, Sequencing,\nFunctionalPrediction, Coverage, Transcriptomics", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libbz2-dev libicu-dev liblzma-dev xz-utils\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:04:19 UTC", "RemoteUrl": "https://github.com/bioc/PICB", "RemoteRef": "HEAD", "RemoteSha": "a70935e5e9ebafb35e4f409860f2d6b61ccf9757", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 10:19:06 UTC", "User": "root" }, "Author": "Pavol Genzor [aut],\nAleksandr Friman [aut],\nDaniel Stoyko [aut],\nParthena Konstantinidou [aut],\nFranziska Ahrend [aut, cre] (ORCID:\n),\nZuzana Loubalova [aut],\nYuejun Wang [aut],\nHernan Lorenzi [aut],\nAstrid D Haase [aut]", "Maintainer": "Franziska Ahrend ", "MD5sum": "db023e8e9d5dd05ac683e4b433126fb6", "_user": "bioc", "_type": "src", "_file": "PICB_1.5.0.tar.gz", "_fileid": "96b6f952bfa9e821d6c5a9eae0cc1964783266517134ac2266c28fd301426e4a", "_filesize": 4737793, "_sha256": "96b6f952bfa9e821d6c5a9eae0cc1964783266517134ac2266c28fd301426e4a", "_created": "2026-05-31T10:19:06.000Z", "_published": "2026-05-31T10:28:56.417Z", "_jobs": [ { "job": 78718147202, "time": 209, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7315931238" }, { "job": 78718147196, "time": 518, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7315960457" }, { "job": 78718147211, "time": 550, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7315963776" }, { "job": 78718147206, "time": 421, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7315951041" }, { "job": 78718147203, "time": 491, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7315957856" }, { "job": 78717852372, "time": 321, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7315910013" }, { "job": 78718147201, "time": 157, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7315926352" }, { "job": 78718147195, "time": 388, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7315948142" }, { "job": 78718147200, "time": 508, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7315959494" }, { "job": 78718147199, "time": 501, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7315958977" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26709823324", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/PICB", "_commit": { "id": "a70935e5e9ebafb35e4f409860f2d6b61ccf9757", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381459 }, "_maintainer": { "name": "Franziska Ahrend", "email": "haase-lab-bioinfo@nih.gov" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "utils", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "GenomicAlignments", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "seqinr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "openxlsx", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rtracklayer", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "prettydoc", "role": "Suggests" }, { "package": "BSgenome", "role": "Suggests" }, { "package": "BSgenome.Dmelanogaster.UCSC.dm6", "role": "Suggests" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-31", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.5.0", "bioc": "3.24" }, { "branch": "release", "version": "1.4.0", "bioc": "3.23" } ], "_topics": [ "genetics", "genomeannotation", "sequencing", "functionalprediction", "coverage", "transcriptomics" ], "_stars": 8, "_contributors": [ { "user": "frahrend", "count": 44, "uuid": 15805954 }, { "user": "alexfriman", "count": 12, "uuid": 20302553 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 257, "source": "https://www.bioconductor.org/packages/stats/bioc/PICB" }, "_devurl": "https://github.com/haaselab/picb", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PICB.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/haaselab/picb", "_realowner": "bioc", "_cranurl": false, "_exports": [ "PICBannotate", "PICBbuild", "PICBexporttoexcel", "PICBgetchromosomes", "PICBimportfromexcel", "PICBload", "PICBloadfasta", "PICBoptimize", "PICBstrandanalysis" ], "_help": [ { "page": "PICBannotate", "title": "Annotate GRanges according to a piRNA library", "topics": [ "PICBannotate" ] }, { "page": "PICBbuild", "title": "Build piRNA seeds/cores/clusters from alignments", "topics": [ "PICBbuild" ] }, { "page": "PICBexporttoexcel", "title": "Export cluster object into an Excel file", "topics": [ "PICBexporttoexcel" ] }, { "page": "PICBgetchromosomes", "title": "Get SeqInfo object from standard non-circular chromosome names from your genome", "topics": [ "PICBgetchromosomes" ] }, { "page": "PICBimportfromexcel", "title": "Import cluster object from an Excel file", "topics": [ "PICBimportfromexcel" ] }, { "page": "PICBload", "title": "Load and preprocess BAM files containing piRNA alignments", "topics": [ "PICBload" ] }, { "page": "PICBloadfasta", "title": "Get SeqInfo object from a fasta file", "topics": [ "PICBloadfasta" ] }, { "page": "PICBoptimize", "title": "Runs PICBbuild multiple times with provided parameters and returns optimization data frame.", "topics": [ "PICBoptimize" ] }, { "page": "PICBstrandanalysis", "title": "Add sense/antisense ratio of unique piRNAs per piRNA cluster", "topics": [ "PICBstrandanalysis" ] } ], "_readme": "https://github.com/bioc/PICB/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bitops", "cigarillo", "cli", "codetools", "cpp11", "crayon", "data.table", "DelayedArray", "dplyr", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "glue", "IRanges", "lambda.r", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "nlme", "openxlsx", "pillar", "pixmap", "pkgconfig", "R6", "Rcpp", "RcppArmadillo", "Rhtslib", "rlang", "Rsamtools", "S4Arrays", "S4Vectors", "segmented", "Seqinfo", "seqinr", "snow", "sp", "SparseArray", "stringi", "SummarizedExperiment", "tibble", "tidyselect", "utf8", "vctrs", "withr", "XVector", "zip" ], "_vignettes": [ { "source": "PICB.Rmd", "filename": "PICB.html", "title": "Introduction to the piRNA Cluster Builder (PICB)", "author": "Haase Lab", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting Started", "How to run PICB", "BAM File Requirements", "Information on the demo dataset", "Reference Genome", "Running PICB", "Load Alignments with PICBload", "Build piRNA Clusters with PICBbuild", "Optimize parameters with PICBoptimize", "Strand-specific analysis with PICBstrandanalysis", "Explore Results", "Export Results", "Import Results", "Parameter Adjustments", "Parameters for PICBload", "Parameters for PICBbuild", "Output", "Metadata Columns", "Acknowledgments", "Session Information" ], "created": "2025-01-22 18:31:36", "modified": "2025-07-31 18:48:56", "commits": 3 } ], "_score": 5.079181246047625, "_indexed": true, "_nocasepkg": "picb", "_universes": [ "bioc", "haaselab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.0", "date": "2026-05-31T10:22:53.000Z", "distro": "noble", "commit": "a70935e5e9ebafb35e4f409860f2d6b61ccf9757", "fileid": "6d6fd9ba5616c9c025e414deb5ffb4061a39283bc4cb049e64bb7360cb77090b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26709823324" }, { "r": "4.6.0", "os": "linux", "version": "1.5.0", "date": "2026-05-31T10:23:20.000Z", "distro": "noble", "commit": "a70935e5e9ebafb35e4f409860f2d6b61ccf9757", "fileid": "ed6b205df751882fe5e2e51cdc5fb4753b52a716e28d41c3df9391e4ad458646", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26709823324" }, { "r": "4.5.3", "os": "mac", "version": "1.5.0", "date": "2026-05-31T10:21:00.000Z", "commit": "a70935e5e9ebafb35e4f409860f2d6b61ccf9757", "fileid": "b78332c9d23ba4efb58c3312804f8fff68fc13b33888b45c02b000ea6caa22bf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26709823324" }, { "r": "4.6.0", "os": "mac", "version": "1.5.0", "date": "2026-05-31T10:21:03.000Z", "commit": "a70935e5e9ebafb35e4f409860f2d6b61ccf9757", "fileid": "e202909748b3abc94a70f423a6f9c3e7c54e61d37a28724cd09f409ed1892d3c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26709823324" }, { "r": "4.6.0", "os": "wasm", "version": "1.5.0", "date": "2026-05-31T10:22:03.000Z", "commit": "a70935e5e9ebafb35e4f409860f2d6b61ccf9757", "fileid": "42f707e2eb3dc6687360b19d3e8a2637e0b222814b4d8794c29e55328b4a5db2", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26709823324" }, { "r": "4.7.0", "os": "win", "version": "1.5.0", "date": "2026-05-31T10:21:34.000Z", "commit": "a70935e5e9ebafb35e4f409860f2d6b61ccf9757", "fileid": "487fde65c931d3dbbeb578501840237531e95847a41b7538c29834d2525dc14f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26709823324" }, { "r": "4.5.3", "os": "win", "version": "1.5.0", "date": "2026-05-31T10:21:32.000Z", "commit": "a70935e5e9ebafb35e4f409860f2d6b61ccf9757", "fileid": "86e101293ff337ee1844f4bc8f67c1d518f17808bc7796f3d57ebf8ec6290da7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26709823324" }, { "r": "4.6.0", "os": "win", "version": "1.5.0", "date": "2026-05-31T10:21:36.000Z", "commit": "a70935e5e9ebafb35e4f409860f2d6b61ccf9757", "fileid": "27ec1073c796bec2da29f1b7d3fea5ef69881aebd16bd817220d787a5b9163ec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26709823324" } ] }