{ "_id": "6a12988bacfb0bcc41d0d101", "Package": "h5vc", "Type": "Package", "Title": "Managing alignment tallies using a hdf5 backend", "Version": "2.46.0", "Author": "Paul Theodor Pyl", "Maintainer": "Paul Theodor Pyl ", "Description": "This package contains functions to interact with tally\ndata from NGS experiments that is stored in HDF5 files.", "License": "GPL (>= 3)", "VignetteBuilder": "knitr", "SystemRequirements": "GNU make", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:38:24 UTC", "RemoteUrl": "https://git.bioconductor.org/packages/h5vc", "RemoteRef": "RELEASE_3_23", "RemoteSha": "c99f423530785192131b2813253a06864e922162", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-24 06:06:57 UTC", "User": "root" }, "MD5sum": "fd49af514943fa279d1e8e0979bb612d", "_user": "bioc-release", "_type": "src", "_file": "h5vc_2.46.0.tar.gz", "_fileid": "d449d017acc15f5735dbf349d2733ad5c586f4a9d12cab22089bb8cdfb83d262", "_filesize": 1485911, "_sha256": "d449d017acc15f5735dbf349d2733ad5c586f4a9d12cab22089bb8cdfb83d262", "_created": "2026-05-24T06:06:57.000Z", "_published": "2026-05-24T06:19:54.999Z", "_jobs": [ { "job": 77576231505, "time": 296, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7182774327" }, { "job": 77576231569, "time": 368, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7182781419" }, { "job": 77576231531, "time": 449, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7182789153" }, { "job": 77576231558, "time": 360, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7182780932" }, { "job": 77576231544, "time": 416, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7182785978" }, { "job": 77576231512, "time": 249, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7182769637" }, { "job": 77576231521, "time": 446, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7182788969" }, { "job": 77576231549, "time": 208, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7182765212" }, { "job": 77576231527, "time": 506, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7182794819" }, { "job": 77575728066, "time": 524, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7182742646" }, { "job": 77576231501, "time": 257, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 77576231526, "time": 647, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7182808692" }, { "job": 77576231510, "time": 727, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7182817165" }, { "job": 77576231502, "time": 666, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7182810955" } ], "_bioccheck": { "error": 3, "warning": 6, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://git.bioconductor.org/packages/h5vc", "_commit": { "id": "c99f423530785192131b2813253a06864e922162", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379904 }, "_maintainer": { "name": "Paul Theodor Pyl", "email": "paul.theodor.pyl@gmail.com", "login": "paulpyl", "description": "", "uuid": 12493460 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "grid", "role": "Depends" }, { "package": "gridExtra", "role": "Depends" }, { "package": "ggplot2", "role": "Depends" }, { "package": "Rhtslib", "version": ">= 1.99.1", "role": "LinkingTo" }, { "package": "rhdf5", "role": "Imports" }, { "package": "reshape", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "Rsamtools", "version": ">= 2.13.1", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "abind", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "BatchJobs", "role": "Imports" }, { "package": "h5vcData", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "locfit", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" }, { "package": "biomaRt", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.NCBI.GRCh38", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.47.0", "bioc": "3.24" }, { "branch": "release", "version": "2.46.0", "bioc": "3.23" } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 494, "source": "https://www.bioconductor.org/packages/stats/bioc/h5vc" }, "_mentions": 1, "_searchresults": 4, "_topics": [ "curl", "bzip2", "xz-utils", "zlib", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/h5vc.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "applyTallies", "bases", "batchTallies", "batchTallyParam", "binGenome", "binnedAFs", "binnedCoverage", "callVariantsPaired", "callVariantsPairedFisher", "callVariantsSingle", "collectTallies", "defineBlocks", "encodeDNAString", "formatGenomicPosition", "geom_h5vc", "getChromSize", "getSampleData", "h5dapply", "h5readBlock", "mergeTallies", "mergeTallyFiles", "mismatchPlot", "mutationSpectrum", "plotMutationSpectrum", "prepareForHDF5", "prepareTallyFile", "rerunBatchTallies", "resizeCohort", "setSampleData", "tallyBAM", "tallyRanges", "tallyRangesBatch", "tallyRangesToFile", "vcConfParams", "writeReference", "writeToTallyFile" ], "_datasets": [ { "name": "bases", "title": "Mutation spectrum analyses", "object": "bases", "file": "bases.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "h5vc-package", "title": "Managing alignment tallies using a hdf5 backend", "topics": [ "h5vc-package", "h5vc" ] }, { "page": "applyTallies", "title": "Preparing the results of tallyBAM for writing to an HDF5 tally file", "topics": [ "applyTallies" ] }, { "page": "batchTallies", "title": "Tallying bam files in parallel using 'BatchJobs' on high performance compute clusters (HPC)", "topics": [ "batchTallies", "batchTallyParam", "collectTallies", "rerunBatchTallies" ] }, { "page": "binGenome", "title": "Function for binning a genome.", "topics": [ "binGenome" ] }, { "page": "binnedAFs", "title": "Estimate allelic frequency distributions in bins along the genome", "topics": [ "binnedAFs" ] }, { "page": "callVariants", "title": "Variant calling", "topics": [ "callDeletionsPaired", "callVariantsPaired", "vcConfParams" ] }, { "page": "callVariantsFisher", "title": "Paired variant calling using fisher tests", "topics": [ "callVariantsPairedFisher" ] }, { "page": "callVariantsSingle", "title": "Single sample variant calling", "topics": [ "callVariantsSingle" ] }, { "page": "coverage", "title": "Coverage analysis", "topics": [ "binnedCoverage" ] }, { "page": "geom_h5vc", "title": "geom_h5vc", "topics": [ "geom_h5vc" ] }, { "page": "getSampleData", "title": "Reading and writing sample data from / to a tally file", "topics": [ "getSampleData", "setSampleData" ] }, { "page": "h5dapply", "title": "h5dapply", "topics": [ "h5dapply", "h5dapply,GRanges-method", "h5dapply,IRanges-method", "h5dapply,numeric-method" ] }, { "page": "h5readBlock", "title": "h5readBlock", "topics": [ "h5readBlock" ] }, { "page": "helpers", "title": "helper functions", "topics": [ "defineBlocks", "encodeDNAString", "formatGenomicPosition", "getChromSize" ] }, { "page": "mergeTallies", "title": "Merging the prepared results from multiple bam file tallies into one block that can be written to the HDF5 tally file", "topics": [ "mergeTallies" ] }, { "page": "mergeTallyFiles", "title": "Merging multiple tally files into one", "topics": [ "mergeTallyFiles" ] }, { "page": "mismatchPlot", "title": "mismatchPlot", "topics": [ "mismatchPlot" ] }, { "page": "mutationSpectrum", "title": "Mutation spectrum analyses", "topics": [ "bases", "mutationSpectrum", "variantCalls" ] }, { "page": "plotMutationSpectrum", "title": "Plotting a mutation spectrum", "topics": [ "plotMutationSpectrum" ] }, { "page": "prepareForHDF5", "title": "Preparing the results of tallyBAM for writing to an HDF5 tally file", "topics": [ "prepareForHDF5" ] }, { "page": "prepareTallyFile", "title": "prepareTallyFile", "topics": [ "prepareTallyFile", "resizeCohort" ] }, { "page": "tallyBAM", "title": "tallyBAM", "topics": [ "tallyBAM" ] }, { "page": "tallyRanges", "title": "Tallying function with a 'GRanges' interface.", "topics": [ "tallyRanges", "tallyRangesBatch", "tallyRangesToFile" ] }, { "page": "writeReference", "title": "Filling the Reference dataset in a tally file from a DNAString", "topics": [ "writeReference" ] }, { "page": "writeToTallyFile", "title": "Writing data to an HDF5 tally file", "topics": [ "writeToTallyFile" ] } ], "_rundeps": [ "abind", "askpass", "backports", "base64enc", "BatchJobs", "BBmisc", "BH", "BiocGenerics", "biocmake", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "brew", "cachem", "checkmate", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "digest", "dir.expiry", "farver", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "h5vcData", "httr", "IRanges", "isoband", "jsonlite", "labeling", "lambda.r", "lifecycle", "memoise", "mime", "openssl", "pkgconfig", "plyr", "R6", "RColorBrewer", "Rcpp", "reshape", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rlang", "Rsamtools", "RSQLite", "S4Vectors", "S7", "scales", "sendmailR", "Seqinfo", "snow", "stringi", "sys", "UCSC.utils", "vctrs", "viridisLite", "withr", "XVector" ], "_sysdeps": [ { "shlib": "libcurl", "package": "libcurl4t64", "headers": "libcurl4-openssl-dev", "source": "curl", "version": "8.5.0-2ubuntu10.9", "name": "curl", "homepage": "https://curl.se/", "description": "easy-to-use client-side URL transfer library (OpenSSL flavour)" }, { "shlib": "libbz2", "package": "libbz2-1.0", "headers": "libbz2-dev", "source": "bzip2", "version": "1.0.8-5.1build0.1", "name": "bzip2", "homepage": "https://sourceware.org/bzip2/", "description": "high-quality block-sorting file compressor library - runtime" }, { "shlib": "liblzma", "package": "liblzma5", "headers": "liblzma-dev", "source": "xz-utils", "version": "5.6.1+really5.4.5-1ubuntu0.2", "name": "xz-utils", "homepage": "https://tukaani.org/xz/", "description": "XZ-format compression library" }, { "shlib": "libz", "package": "zlib1g", "headers": "zlib1g-dev", "source": "zlib", "version": "1:1.3.dfsg-3.1ubuntu2.1", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "h5vc.simple.genome.browser.Rmd", "filename": "h5vc.simple.genome.browser.html", "title": "Building a minimal genome browser with h5vc and shiny", "engine": "knitr::rmarkdown", "headings": [ "Building a minimal genome browser with h5vc and shiny", "Prerequisites", "The Data", "The Shiny App", "ui.R", "server.R", "Including Variant Calls", "Calling the variants", "Extending the functionality of the genome browser", "Changes to the interface", "Changes to the server-side computations", "Conclusions" ], "created": "2013-09-24 11:13:41", "modified": "2019-02-12 15:46:29", "commits": 5 }, { "source": "h5vc.tour.Rmd", "filename": "h5vc.tour.html", "title": "h5vc -- Tour", "engine": "knitr::rmarkdown", "headings": [ "h5vc -- Scalabale nucleotide tallies using HDF5", "Motivation", "Nucleotide Tally Definition", "A practical example", "Ranges interface", "Creating tally files", "Extracting tallies from the bam files", "Checking if everything worked", "Mutation Spectrum Analysis", "Parallelisation", "Using Clusters" ], "created": "2014-01-28 10:40:37", "modified": "2025-01-22 13:53:03", "commits": 23 } ], "_score": 3.6020599913279625, "_indexed": false, "_nocasepkg": "h5vc", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/h5vc", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.46.0", "date": "2026-05-24T06:11:35.000Z", "distro": "noble", "arch": "aarch64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "67b16f130327736048930f619f018aa949451db8c14d569a7018e48639788993", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" }, { "r": "4.7.0", "os": "linux", "version": "2.46.0", "date": "2026-05-24T06:12:39.000Z", "distro": "noble", "arch": "x86_64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "39f2336f5f74b9eb3c096b9d4772e1bb9b5f3f41ca3621380750de98dc5ca952", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" }, { "r": "4.6.0", "os": "linux", "version": "2.46.0", "date": "2026-05-24T06:11:35.000Z", "distro": "noble", "arch": "aarch64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "a15d8a6a56abdb61a6c625ab6ef603e9b6c195b7e0277b3683ef1cf64e9f8bf4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" }, { "r": "4.6.0", "os": "linux", "version": "2.46.0", "date": "2026-05-24T06:12:05.000Z", "distro": "noble", "arch": "x86_64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "9cf8313e2c1f5591e310ccb21b77251450a560cf8913f1ca0606d22d19b59bf8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" }, { "r": "4.5.3", "os": "mac", "version": "2.46.0", "date": "2026-05-24T06:10:08.000Z", "arch": "aarch64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "746f242b6f5d50e929a68217650aeb15abb8633a4dbe917cd310f3ac84026cc7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" }, { "r": "4.5.3", "os": "mac", "version": "2.46.0", "date": "2026-05-24T06:12:05.000Z", "arch": "x86_64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "7c96dccf6f4133cd3c31717cae14093e13ade7fd49ae13241e8098b061b71d66", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" }, { "r": "4.6.0", "os": "mac", "version": "2.46.0", "date": "2026-05-24T06:09:34.000Z", "arch": "aarch64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "854b16b81ae571167ad8eda4e1f3a12fbc930bd8fb3b356f7e2c9aff139fc90b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" }, { "r": "4.6.0", "os": "mac", "version": "2.46.0", "date": "2026-05-24T06:12:34.000Z", "arch": "x86_64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "f924022739a5b5bc9483a9c649771de638dd277734cc538be8fe806e74d422cd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" }, { "r": "4.7.0", "os": "win", "version": "2.46.0", "date": "2026-05-24T06:14:37.000Z", "arch": "x86_64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "b573d1610007658fc669a703a6cec34191db94589361233fa13d56aa4ab897bf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" }, { "r": "4.5.3", "os": "win", "version": "2.46.0", "date": "2026-05-24T06:14:58.000Z", "arch": "x86_64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "62943c14132fe8cf5a131b36c069c3592b8b9ddc0608ffd0048250affae84de8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" }, { "r": "4.6.0", "os": "win", "version": "2.46.0", "date": "2026-05-24T06:14:51.000Z", "arch": "x86_64", "commit": "c99f423530785192131b2813253a06864e922162", "fileid": "0e7dd054377b91508bd89bf958a734df6f207ac7ab71f76c572f83c8d5a4364b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26353466191" } ] }