{ "_id": "6a494aaff6c47c4419498c2a", "Package": "strandCheckR", "Type": "Package", "Title": "Calculate strandness information of a bam file", "Version": "1.31.0", "Authors@R": "c(\nperson(\"Thu-Hien\", \"To\", email = \"tothuhien@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\n\"Stevie\", \"Pederson\",\nemail = \"stephen.pederson.au@gmail.com\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-8197-3303\")\n)\n)", "Maintainer": "Thu-Hien To ", "Description": "This package aims to quantify and remove putative double\nstrand DNA from a strand-specific RNA sample. There are also\noptions and methods to plot the positive/negative proportions\nof all sliding windows, which allow users to have an idea of\nhow much the sample was contaminated and the appropriate\nthreshold to be used for filtering.", "URL": "https://github.com/UofABioinformaticsHub/strandCheckR", "BugReports": "https://github.com/UofABioinformaticsHub/strandCheckR/issues", "License": "GPL (>= 2)", "Encoding": "UTF-8", "biocViews": "RNASeq, Alignment, QualityControl, Coverage, ImmunoOncology", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:48:23 UTC", "RemoteUrl": "https://github.com/bioc/strandCheckR", "RemoteRef": "HEAD", "RemoteSha": "03d5abbba66188f486f41ecf734a1d50f0aa5e11", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 16:37:59 UTC", "User": "root" }, "Author": "Thu-Hien To [aut, cre],\nStevie Pederson [aut] (ORCID: )", "_user": "bioc", "_type": "src", "_file": "strandCheckR_1.31.0.tar.gz", "_fileid": "https://r2.ropensci.org/04920b8fd4f353d7a63b363e49dbe53445e76808329922e334081766c7331b92", "_filesize": 1199946, "_sha256": "04920b8fd4f353d7a63b363e49dbe53445e76808329922e334081766c7331b92", "_expires": "2026-10-12T18:02:22.000Z", "_created": "2026-07-03T16:37:59.000Z", "_published": "2026-07-04T18:02:23.828Z", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28672833815", "_status": "success", "_upstream": "https://github.com/bioc/strandCheckR", "_commit": { "id": "03d5abbba66188f486f41ecf734a1d50f0aa5e11", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380503 }, "_maintainer": { "name": "Thu-Hien To", "email": "tothuhien@gmail.com", "login": "tothuhien", "description": "Norwegian University of Life Sciences", "uuid": 14748898 }, "_distro": "resolute", "_jobs": [ { "job": 85154535698, "time": 236, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8071430123" }, { "job": 85154535785, "time": 412, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8071475651" }, { "job": 85154535795, "time": 367, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8071463807" }, { "job": 85154535838, "time": 353, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8071460055" }, { "job": 85154535754, "time": 280, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8071441552" }, { "job": 85154535505, "time": 338, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8071368640" }, { "job": 85154535763, "time": 220, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8071426012" }, { "job": 85154535714, "time": 691, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8071548556" }, { "job": 85154535823, "time": 613, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8071528647" }, { "job": 85154535816, "time": 652, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8071536486" } ], "_registered": true, "_dependencies": [ { "package": "ggplot2", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Rsamtools", "role": "Depends" }, { "package": "S4Vectors", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicAlignments", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "TxDb.Hsapiens.UCSC.hg38.knownGene", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "magrittr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-41", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23" } ], "_topics": [ "rnaseq", "alignment", "qualitycontrol", "coverage", "immunooncology" ], "_stars": 1, "_contributors": [ { "user": "tothuhien", "count": 187, "uuid": 14748898 }, { "user": "smped", "count": 34, "uuid": 8252496 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "hpages", "count": 1, "uuid": 8810451 }, { "user": "link-ny", "count": 1, "uuid": 4392950 }, { "user": "rmflight", "count": 1, "uuid": 1509626 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/uofabioinformaticshub/strandcheckr", "_searchresults": 13, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "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/strandCheckR.html", "manual.pdf" ], "_homeurl": "https://github.com/uofabioinformaticshub/strandcheckr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "checkPairedEnd", "filterDNA", "getStrandFromBamFile", "getStrandFromReadInfo", "getWinOverlapEachIRange", "getWinOverlapEachReadFragment", "getWinOverlapGRanges", "intersectWithFeature", "plotHist", "plotWin" ], "_help": [ { "page": "checkPairedEnd", "title": "Test whether a bam file is single-end or paired-end", "topics": [ "checkPairedEnd" ] }, { "page": "filterDNA", "title": "Filter reads comming from double strand sequences from a bam File", "topics": [ "filterDNA" ] }, { "page": "getStrandFromBamFile", "title": "Get the strand information of all windows from bam files", "topics": [ "getStrandFromBamFile" ] }, { "page": "getStrandFromReadInfo", "title": "Get the strand information of all windows from read information", "topics": [ "getStrandFromReadInfo" ] }, { "page": "getWinOverlapEachIRange", "title": "Get the ranges of sliding windows that overlap each range of an IRanges object.", "topics": [ "getWinOverlapEachIRange" ] }, { "page": "getWinOverlapEachReadFragment", "title": "Get the window ranges that overlap each read fragment", "topics": [ "getWinOverlapEachReadFragment" ] }, { "page": "getWinOverlapGRanges", "title": "Get the sliding windows that overlap a GRanges object", "topics": [ "getWinOverlapGRanges" ] }, { "page": "intersectWithFeature", "title": "Intersect the windows data frame with an annotation data frame", "topics": [ "intersectWithFeature" ] }, { "page": "plotHist", "title": "Plot the histogram of positive proportions", "topics": [ "plotHist" ] }, { "page": "plotWin", "title": "Plot the number of reads vs the proportion of '+' stranded reads.", "topics": [ "plotWin" ] } ], "_readme": "https://github.com/bioc/strandCheckR/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "dplyr", "farver", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "httr", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "plyr", "png", "R6", "RColorBrewer", "Rcpp", "RCurl", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyselect", "TxDb.Hsapiens.UCSC.hg38.knownGene", "utf8", "vctrs", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "strandCheckR.Rmd", "filename": "strandCheckR.html", "title": "An Introduction To strandCheckR", "author": "Thu-Hien To, Stevie Pederson", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Get windows information", "Intersect with an annotation GRanges object", "Plot histogram and windows information", "Filter bam files", "Session Info" ], "created": "2018-05-24 00:22:40", "modified": "2025-03-21 14:25:42", "commits": 33 } ], "_score": 5.260071387985075, "_indexed": true, "_nocasepkg": "strandcheckr", "_universes": [ "bioc", "tothuhien", "uofabioinformaticshub" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-07-03T16:42:10.000Z", "distro": "resolute", "commit": "03d5abbba66188f486f41ecf734a1d50f0aa5e11", "fileid": "https://r2.ropensci.org/db8f282730ad5b5a5b40bf5ca5a95c696658810236a21f6f27c9ee498c3a3d96", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28672833815" }, { "r": "4.6.1", "os": "linux", "version": "1.31.0", "date": "2026-07-03T16:42:06.000Z", "distro": "resolute", "commit": "03d5abbba66188f486f41ecf734a1d50f0aa5e11", "fileid": "https://r2.ropensci.org/529546256c4e6f2134f818a9c5d8b96d037711f2db656162c88810ad42b79ab7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28672833815" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-07-03T16:41:14.000Z", "commit": "03d5abbba66188f486f41ecf734a1d50f0aa5e11", "fileid": "https://r2.ropensci.org/8785081696d78f17d5fa06a53f93d57aaf6d9277dcf7d97394476afc0f5fc03e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28672833815" }, { "r": "4.6.1", "os": "mac", "version": "1.31.0", "date": "2026-07-03T16:40:25.000Z", "commit": "03d5abbba66188f486f41ecf734a1d50f0aa5e11", "fileid": "https://r2.ropensci.org/f361fe12b26885ae196b65e42209ed966cff0a1f60768fcd0b307cfe0f2c3d1c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28672833815" }, { "r": "4.6.0", "os": "wasm", "version": "1.31.0", "date": "2026-07-03T16:42:18.000Z", "commit": "03d5abbba66188f486f41ecf734a1d50f0aa5e11", "fileid": "https://r2.ropensci.org/a86d26cd6647fa947fa0c2a89b8601c1137b4f9ce1084880faad9c560ce262d9", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28672833815" }, { "r": "4.7.0", "os": "win", "version": "1.31.0", "date": "2026-07-03T16:45:39.000Z", "commit": "03d5abbba66188f486f41ecf734a1d50f0aa5e11", "fileid": "https://r2.ropensci.org/7392fe5a7e2b9275cc3473e2e0af1a1125a73a4deeafcc7f1a98c6240acca058", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28672833815" }, { "r": "4.5.3", "os": "win", "version": "1.31.0", "date": "2026-07-03T16:45:17.000Z", "commit": "03d5abbba66188f486f41ecf734a1d50f0aa5e11", "fileid": "https://r2.ropensci.org/e79ebcb1d91dd90f3b6d6c4a91a82fef9fb71bb79bd69901139a05cb29b20ac3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28672833815" }, { "r": "4.6.1", "os": "win", "version": "1.31.0", "date": "2026-07-03T16:45:27.000Z", "commit": "03d5abbba66188f486f41ecf734a1d50f0aa5e11", "fileid": "https://r2.ropensci.org/45471babc1d1227c2d4b871a29cf3dbd12dfc6421442f14b5be66d0b01bb2310", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28672833815" } ] }