{ "_id": "6a49428b18cdde069385e685", "Package": "borealis", "Type": "Package", "Title": "Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution", "Version": "1.17.0", "Authors@R": "person(given = \"Garrett\",\nfamily = \"Jenkinson\",\nrole = c(\"aut\", \"cre\"),\nemail = \"gargar934@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2548-098X\"))", "Description": "Borealis is an R library performing outlier analysis for\ncount-based bisulfite sequencing data. It detectes outlier\nmethylated CpG sites from bisulfite sequencing (BS-seq). The\ncore of Borealis is modeling Beta-Binomial distributions. This\ncan be useful for rare disease diagnoses.", "License": "GPL-3", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "biocViews": "Sequencing, Coverage, DNAMethylation,\nDifferentialMethylation", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:15 UTC", "RemoteUrl": "https://github.com/bioc/borealis", "RemoteRef": "HEAD", "RemoteSha": "7bbd4fbc10baba4b64832ef78df75eaaa425f0df", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 09:42:47 UTC", "User": "root" }, "Author": "Garrett Jenkinson [aut, cre] (ORCID:\n)", "Maintainer": "Garrett Jenkinson ", "_user": "bioc", "_type": "src", "_file": "borealis_1.17.0.tar.gz", "_fileid": "https://r2.ropensci.org/280a99e61db417af85f5c2707faa3aabc9e915d085154c726092e1d7d19f7966", "_filesize": 193149, "_sha256": "280a99e61db417af85f5c2707faa3aabc9e915d085154c726092e1d7d19f7966", "_expires": "2026-10-12T17:27:37.000Z", "_created": "2026-07-04T09:42:47.000Z", "_published": "2026-07-04T17:27:39.077Z", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28702136043", "_status": "failure", "_upstream": "https://github.com/bioc/borealis", "_commit": { "id": "7bbd4fbc10baba4b64832ef78df75eaaa425f0df", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381095 }, "_maintainer": { "name": "Garrett Jenkinson", "email": "gargar934@gmail.com", "login": "garrettjenkinson", "description": "", "uuid": 12863507, "orcid": "0000-0003-2548-098X" }, "_distro": "resolute", "_jobs": [ { "job": 85152182057, "time": 273, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8080593641" }, { "job": 85152182042, "time": 491, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8080619993" }, { "job": 85152182227, "time": 527, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8080624408" }, { "job": 85152182187, "time": 295, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8080890086" }, { "job": 85152182097, "time": 296, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8080896278" }, { "job": 85152182041, "time": 422, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "8080559589" }, { "job": 85152182076, "time": 245, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8080590092" }, { "job": 85152182034, "time": 344, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8080602016" }, { "job": 85152182019, "time": 380, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8080606577" }, { "job": 85152182192, "time": 365, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8080604546" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "doParallel", "role": "Imports" }, { "package": "snow", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "gamlss", "role": "Imports" }, { "package": "gamlss.dist", "role": "Imports" }, { "package": "bsseq", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "DSS", "role": "Imports" }, { "package": "R.utils", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "annotatr", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.17.0", "bioc": "3.24" }, { "branch": "release", "version": "1.16.0", "bioc": "3.23" } ], "_topics": [ "sequencing", "coverage", "dnamethylation", "differentialmethylation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 18, "_rbuild": "4.6.1", "_assets": [ "extra/borealis.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "plotCpGsite", "runBorealis", "runSingleNewSample" ], "_help": [ { "page": "borealis-package", "title": "Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution", "topics": [ "borealis-package", "borealis" ] }, { "page": "plotCpGsite", "title": "Generate a plot of the model and raw data at one or more CpG sites", "topics": [ "plotCpGsite" ] }, { "page": "runBorealis", "title": "Run the full borealis pipeline", "topics": [ "runBorealis" ] }, { "page": "runSingleNewSample", "title": "Run a single new sample after modeling complete", "topics": [ "runSingleNewSample" ] } ], "_rundeps": [ "abind", "askpass", "assorthead", "beachmat", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "biocmake", "BiocParallel", "Biostrings", "bitops", "BSgenome", "bsseq", "cigarillo", "cli", "codetools", "cowplot", "cpp11", "crayon", "curl", "data.table", "DelayedArray", "DelayedMatrixStats", "dir.expiry", "doParallel", "dplyr", "DSS", "farver", "filelock", "foreach", "formatR", "futile.logger", "futile.options", "gamlss", "gamlss.data", "gamlss.dist", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gtable", "gtools", "h5mread", "HDF5Array", "httr", "IRanges", "isoband", "iterators", "jsonlite", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mime", "nlme", "openssl", "permute", "pillar", "pkgconfig", "plyr", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "RColorBrewer", "Rcpp", "RCurl", "restfulr", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "sparseMatrixStats", "statmod", "SummarizedExperiment", "survival", "sys", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_score": 2.5563025007672873, "_indexed": true, "_nocasepkg": "borealis", "_universes": [ "bioc", "garrettjenkinson" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.0", "date": "2026-07-04T09:47:38.000Z", "distro": "resolute", "commit": "7bbd4fbc10baba4b64832ef78df75eaaa425f0df", "fileid": "https://r2.ropensci.org/69501beb9a32b48f1838951a531506a197e53d1bcb121499826501371c0faa61", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28702136043" }, { "r": "4.6.1", "os": "linux", "version": "1.17.0", "date": "2026-07-04T09:48:21.000Z", "distro": "resolute", "commit": "7bbd4fbc10baba4b64832ef78df75eaaa425f0df", "fileid": "https://r2.ropensci.org/efacb76bcc57585ca7c8dfb7049230a9d4990fa2bdb8f148e08850b26892b324", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28702136043" }, { "r": "4.5.3", "os": "mac", "version": "1.17.0", "date": "2026-07-04T10:29:42.000Z", "commit": "7bbd4fbc10baba4b64832ef78df75eaaa425f0df", "fileid": "https://r2.ropensci.org/ce19371dd6f802b05b6a6924cd622efc55a9ff906b1e002931d9b679778c058f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28702136043" }, { "r": "4.6.1", "os": "mac", "version": "1.17.0", "date": "2026-07-04T10:30:42.000Z", "commit": "7bbd4fbc10baba4b64832ef78df75eaaa425f0df", "fileid": "https://r2.ropensci.org/815a80b55abf9ef9d77e421974eddefec279607175ca7dfc2c638296e0dfe0b3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28702136043" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.0", "date": "2026-07-04T09:47:34.000Z", "commit": "7bbd4fbc10baba4b64832ef78df75eaaa425f0df", "fileid": "https://r2.ropensci.org/4ef470079ea87b2f04c82dd696a0f8641525e4f3274ab01b841a07a02596bba0", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28702136043" }, { "r": "4.7.0", "os": "win", "version": "1.17.0", "date": "2026-07-04T09:45:24.000Z", "commit": "7bbd4fbc10baba4b64832ef78df75eaaa425f0df", "fileid": "https://r2.ropensci.org/9db32682c140d4175cb1edb6ca7f24d4196394f662ae8cae7e012cfd8b842b88", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28702136043" }, { "r": "4.5.3", "os": "win", "version": "1.17.0", "date": "2026-07-04T09:45:50.000Z", "commit": "7bbd4fbc10baba4b64832ef78df75eaaa425f0df", "fileid": "https://r2.ropensci.org/2d6d711dc95faaa2f848e83162b269ed96b3ef078d5bb296e0bec58f0e3d2b0c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28702136043" }, { "r": "4.6.1", "os": "win", "version": "1.17.0", "date": "2026-07-04T09:45:37.000Z", "commit": "7bbd4fbc10baba4b64832ef78df75eaaa425f0df", "fileid": "https://r2.ropensci.org/4bb43da2c7ed6c6b6f3b9c1d43cc8f922db0d02cc2461e0e4365df43648ae3f1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28702136043" } ] }