{ "_id": "6a2fad8b3efcd9bda4327b72", "Package": "IONiseR", "Title": "Quality Assessment Tools for Oxford Nanopore MinION data", "Version": "2.36.0", "Authors@R": "person(\"Mike\", \"Smith\", email = \"grimbough@gmail.com\", role\n= c(\"aut\", \"cre\"))", "Description": "IONiseR provides tools for the quality assessment of\nOxford Nanopore MinION data. It extracts summary statistics\nfrom a set of fast5 files and can be used either before or\nafter base calling. In addition to standard summaries of the\nread-types produced, it provides a number of plots for\nvisualising metrics relative to experiment run time or\nspatially over the surface of a flowcell.", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "biocViews": "QualityControl, DataImport, Sequencing", "NeedsCompilation": "no", "Author": "Mike Smith [aut, cre]", "Maintainer": "Mike Smith ", "RoxygenNote": "6.0.1", "Collate": "'IONiseR.R' 'classes.R' 'Methods-accessors.R'\n'Methods-subsetting.R' 'fast5Readers.R' 'fast5Status.R'\n'fast5readers_summary.R' 'fast5utilities.R' 'fastqProcessing.R'\n'plotting_kmers.R' 'plotting_layout.R'\n'plotting_summaryStats.R' 'processing_bam.R' 'readSummary.R'\n'squiggle.R' 'zzz.R'", "PackageStatus": "Deprecated", "Config/pak/sysreqs": "libbz2-dev libicu-dev libjpeg-dev liblzma-dev\nlibpng-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:41:26 UTC", "RemoteUrl": "https://github.com/bioc/IONiseR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "fac0d66d99989631c56d239030b5847b6e58ccdd", "Packaged": { "Date": "2026-06-15 07:36:44 UTC", "User": "root" }, "MD5sum": "dbff8e044f5791c9c87499e443092641", "_user": "bioc-release", "_type": "src", "_file": "IONiseR_2.36.0.tar.gz", "_fileid": "63cbbd1bebffca94ecb08cdcd22c2cab8abf71b535c947c498669502cbb20591", "_filesize": 1316842, "_sha256": "63cbbd1bebffca94ecb08cdcd22c2cab8abf71b535c947c498669502cbb20591", "_created": "2026-06-15T07:36:44.000Z", "_published": "2026-06-15T07:45:15.469Z", "_jobs": [ { "job": 81369656552, "time": 207, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7631792103" }, { "job": 81369656547, "time": 438, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7631867712" }, { "job": 81369656563, "time": 371, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7631845817" }, { "job": 81369656575, "time": 252, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7631806682" }, { "job": 81369656566, "time": 265, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7631810629" }, { "job": 81368916820, "time": 291, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7631728900" }, { "job": 81369656600, "time": 140, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7631771707" }, { "job": 81369656574, "time": 321, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7631830276" }, { "job": 81369656598, "time": 292, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7631820538" }, { "job": 81369656625, "time": 328, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7631830852" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531015565", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/IONiseR", "_commit": { "id": "fac0d66d99989631c56d239030b5847b6e58ccdd", "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": 1777380086 }, "_maintainer": { "name": "Mike Smith", "email": "grimbough@gmail.com", "login": "grimbough", "description": "Data Engineer at Boehringer-Ingelheim", "uuid": 971237 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4", "role": "Depends" }, { "package": "rhdf5", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "ShortRead", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "XVector", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "bit64", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "minionSummaryData", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-09", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_topics": [ "qualitycontrol", "dataimport", "sequencing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 543, "source": "https://www.bioconductor.org/packages/stats/bioc/IONiseR" }, "_mentions": 2, "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/IONiseR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ "baseCalled", "channelActivityPlot", "channelHeatmap", "eventData", "fast5toFastq", "fastq", "fastq2D", "fastqComplement", "fastqTemplate", "layoutPlot", "plotActiveChannels", "plotBaseProductionRate", "plotCurrentByTime", "plotEventRate", "plotKmerFrequencyCorrelation", "plotReadAccumulation", "plotReadCategoryCounts", "plotReadCategoryQuals", "plotReadTypeProduction", "readFast5Log", "readFast5Summary", "readInfo" ], "_help": [ { "page": "baseCalled", "title": "Extract baseCalled slot", "topics": [ "baseCalled" ] }, { "page": "channelActivityPlot", "title": "Visualise a specified metric over all channels over time.", "topics": [ "channelActivityPlot" ] }, { "page": "channelHeatmap", "title": "Create layout plot of flowcell", "topics": [ "channelHeatmap" ] }, { "page": "eventData", "title": "Extract eventData slot", "topics": [ "eventData" ] }, { "page": "Fast5Summary-class", "title": "An S4 class for summarised data from a MinION sequencing run", "topics": [ "baseCalled,Fast5Summary-method", "eventData,Fast5Summary-method", "Fast5Summary-class", "fastq,Fast5Summary-method", "fastq2D,Fast5Summary-method", "fastqComplement,Fast5Summary-method", "fastqTemplate,Fast5Summary-method", "length,Fast5Summary-method", "readInfo,Fast5Summary-method", "[,Fast5Summary,ANY,ANY,ANY-method" ] }, { "page": "fast5toFastq", "title": "Extract FASTQ files from fast5 files", "topics": [ "fast5toFastq" ] }, { "page": "fastq", "title": "Extract fastq slot", "topics": [ "fastq" ] }, { "page": "fastq2D", "title": "Extract 2D reads", "topics": [ "fastq2D" ] }, { "page": "fastqComplement", "title": "Extract complement reads", "topics": [ "fastqComplement" ] }, { "page": "fastqTemplate", "title": "Extract template reads", "topics": [ "fastqTemplate" ] }, { "page": "IONiseR", "title": "IONiseR: A package for assessing quality of MinION data", "topics": [ "IONiseR-package", "IONiseR" ] }, { "page": "layoutPlot", "title": "Create layout plot of flowcell", "topics": [ "layoutPlot" ] }, { "page": "muxHeatmap", "title": "Create layout plot of flowcell", "topics": [ "muxHeatmap" ] }, { "page": "plotActiveChannels", "title": "Plot the number of active channels for each minute of run time", "topics": [ "plotActiveChannels" ] }, { "page": "plotBaseProductionRate", "title": "Plot the mean rate at which bases are recorded", "topics": [ "plotBaseProductionRate" ] }, { "page": "plotCurrentByTime", "title": "View changes in signal against run time.", "topics": [ "plotCurrentByTime" ] }, { "page": "plotEventRate", "title": "Plot the mean rate at which events occur", "topics": [ "plotEventRate" ] }, { "page": "plotKmerFrequencyCorrelation", "title": "Display correlation between pentemer proportions in two time windows", "topics": [ "plotKmerFrequencyCorrelation" ] }, { "page": "plotReadAccumulation", "title": "Plot the accumulation of reads over the duration of the experiment.", "topics": [ "plotReadAccumulation" ] }, { "page": "plotReadCategoryCounts", "title": "Plot the proportion of template, complement and 2D reads found a dataset.", "topics": [ "plotReadCategoryCounts" ] }, { "page": "plotReadCategoryQuals", "title": "Visualise the mean base quality of each read", "topics": [ "plotReadCategoryQuals" ] }, { "page": "plotReadTypeProduction", "title": "View changes in signal against run time.", "topics": [ "plotReadTypeProduction" ] }, { "page": "readFast5Log", "title": "Read the log entry from a single fast5 file", "topics": [ "readFast5Log" ] }, { "page": "readFast5Summary", "title": "Read summary data from fast5 files.", "topics": [ "readFast5Summary" ] }, { "page": "readInfo", "title": "Extract readInfo slot", "topics": [ "readInfo" ] } ], "_readme": "https://github.com/bioc/IONiseR/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "biocmake", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "cigarillo", "cli", "codetools", "cpp11", "crayon", "DelayedArray", "deldir", "dir.expiry", "dplyr", "farver", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gtable", "hwriter", "interp", "IRanges", "isoband", "jpeg", "labeling", "lambda.r", "lattice", "latticeExtra", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "pillar", "pkgconfig", "png", "purrr", "pwalign", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rlang", "Rsamtools", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "ShortRead", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_score": 2.4771212547196626, "_indexed": false, "_nocasepkg": "ioniser", "_universes": [ "bioc-release" ], "_indexurl": "https://grimbough.r-universe.dev/IONiseR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.36.0", "date": "2026-06-15T07:41:12.000Z", "distro": "noble", "commit": "fac0d66d99989631c56d239030b5847b6e58ccdd", "fileid": "09f626c142f5f9ad27689b3b03e801c516f0a35de416810207a704c728b507d4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531015565" }, { "r": "4.6.0", "os": "linux", "version": "2.36.0", "date": "2026-06-15T07:40:24.000Z", "distro": "noble", "commit": "fac0d66d99989631c56d239030b5847b6e58ccdd", "fileid": "aac95b3453ffd4c61f09e2d6469844ef37ed8fdd447ccd15f97ae1ed5fa1ee0f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531015565" }, { "r": "4.5.3", "os": "mac", "version": "2.36.0", "date": "2026-06-15T07:39:11.000Z", "commit": "fac0d66d99989631c56d239030b5847b6e58ccdd", "fileid": "6ce77459cdbb65d446fe0f4cc64b1d26e71093ce139a50460a5c8abba497865c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531015565" }, { "r": "4.6.0", "os": "mac", "version": "2.36.0", "date": "2026-06-15T07:39:27.000Z", "commit": "fac0d66d99989631c56d239030b5847b6e58ccdd", "fileid": "b4d435ff13a61333981f01b3e3d746dc59a699b53c9f0ee14fb936a86e688e89", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531015565" }, { "r": "4.6.0", "os": "wasm", "version": "2.36.0", "date": "2026-06-15T07:39:42.000Z", "commit": "fac0d66d99989631c56d239030b5847b6e58ccdd", "fileid": "b3fcdfb750e5ea47a8b34ef7e66bd608f2c0041f6678cd930936fc2b80c2d77e", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531015565" }, { "r": "4.7.0", "os": "win", "version": "2.36.0", "date": "2026-06-15T07:39:20.000Z", "commit": "fac0d66d99989631c56d239030b5847b6e58ccdd", "fileid": "057dde7d7aeaa1944f3b211ede5c3584003e21b00b8126779386b9e8a28cab52", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531015565" }, { "r": "4.5.3", "os": "win", "version": "2.36.0", "date": "2026-06-15T07:39:00.000Z", "commit": "fac0d66d99989631c56d239030b5847b6e58ccdd", "fileid": "f7813987c72479ae45de8a38b8af31e0b57facf673581f6cbb788b250c241277", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531015565" }, { "r": "4.6.0", "os": "win", "version": "2.36.0", "date": "2026-06-15T07:39:11.000Z", "commit": "fac0d66d99989631c56d239030b5847b6e58ccdd", "fileid": "46bbfee0adccd2387fed1470425813b8d10672ae801a0c829612eef73dfa0e4f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531015565" } ] }