{ "_id": "6a1bd9f31d7bb097a0a16d5b", "Package": "MDTS", "Title": "Detection of de novo deletion in targeted sequencing trios", "Version": "1.32.0", "Authors@R": "person(\"Jack M..\", \"Fu\", email = \"jmfu@jhsph.edu\", role = c(\"aut\", \"cre\"))", "Description": "A package for the detection of de novo copy number\ndeletions in targeted sequencing of trios with high sensitivity\nand positive predictive value.", "VignetteBuilder": "knitr", "License": "Artistic-2.0", "Encoding": "UTF-8", "RoxygenNote": "6.0.1", "biocViews": "StatisticalMethod, Technology, Sequencing,\nTargetedResequencing, Coverage, DataImport", "Config/pak/sysreqs": "libbz2-dev libicu-dev liblzma-dev xz-utils\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:47:26 UTC", "RemoteUrl": "https://github.com/bioc/MDTS", "RemoteRef": "RELEASE_3_23", "RemoteSha": "0280721d6c808991a93dba8168097ee417304b8e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 06:29:28 UTC", "User": "root" }, "Author": "Jack M.. Fu [aut, cre]", "Maintainer": "Jack M.. Fu ", "MD5sum": "53b1efb6de7d864855ae755f94a89f18", "_user": "bioc-release", "_type": "src", "_file": "MDTS_1.32.0.tar.gz", "_fileid": "cd148e88c65390d57368ff8da3225f6686ff2f695bb42a7b9c9253769a42f3d9", "_filesize": 125270, "_sha256": "cd148e88c65390d57368ff8da3225f6686ff2f695bb42a7b9c9253769a42f3d9", "_created": "2026-05-31T06:29:28.000Z", "_published": "2026-05-31T06:49:23.648Z", "_jobs": [ { "job": 78705621522, "time": 172, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7314451583" }, { "job": 78705621535, "time": 320, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7314467920" }, { "job": 78705621544, "time": 321, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7314468018" }, { "job": 78705621517, "time": 150, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7314550002" }, { "job": 78705621523, "time": 148, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7314555161" }, { "job": 78705431174, "time": 220, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7314432459" }, { "job": 78705621537, "time": 123, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7314445680" }, { "job": 78705621534, "time": 308, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7314466461" }, { "job": 78705621540, "time": 225, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7314457515" }, { "job": 78705621539, "time": 234, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7314458446" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705333179", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MDTS", "_commit": { "id": "0280721d6c808991a93dba8168097ee417304b8e", "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": 1777380446 }, "_maintainer": { "name": "Jack M.. Fu", "email": "jmfu@jhsph.edu", "login": "jmf47", "description": "", "uuid": 5373955 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "GenomicAlignments", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "DNAcopy", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.33.0", "bioc": "3.24" }, { "branch": "release", "version": "1.32.0", "bioc": "3.23" } ], "_topics": [ "statisticalmethod", "technology", "sequencing", "targetedresequencing", "coverage", "dataimport" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 339, "source": "https://www.bioconductor.org/packages/stats/bioc/MDTS" }, "_mentions": 3, "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MDTS.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calcBins", "calcCounts", "calcMD", "denovoDeletions", "getMetaData", "normalizeCounts", "segmentMD", "visualizeDeletion" ], "_help": [ { "page": "MDTS-package", "title": "The MDTS package for Detection of Denovo Deletions from Targeted Sequencing Data Using Minimum-Distance", "topics": [ "MDTS-package", "MDTS" ] }, { "page": "calcBins", "title": "Sample driven calculation of bins for counting", "topics": [ "calcBins" ] }, { "page": "calcCounts", "title": "Creating the raw count matrix", "topics": [ "calcCounts" ] }, { "page": "calcMD", "title": "Calculating the Minimum Distance matrix", "topics": [ "calcMD" ] }, { "page": "denovoDeletions", "title": "Denovo Deletion Calling", "topics": [ "denovoDeletions" ] }, { "page": "getMetaData", "title": "Constructor for metadata", "topics": [ "getMetaData" ] }, { "page": "normalizeCounts", "title": "Calculating the normalized M scores", "topics": [ "normalizeCounts" ] }, { "page": "segmentMD", "title": "Circular Binary Segmentation on Minimum Distances", "topics": [ "segmentMD" ] }, { "page": "visualizeDeletion", "title": "Visualization for deletions", "topics": [ "visualizeDeletion" ] } ], "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bitops", "cigarillo", "cli", "codetools", "cpp11", "crayon", "DelayedArray", "DNAcopy", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "glue", "IRanges", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "Rhtslib", "rlang", "Rsamtools", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "vctrs", "XVector" ], "_score": 2.778151250383644, "_indexed": false, "_nocasepkg": "mdts", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/MDTS", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.32.0", "date": "2026-05-31T06:33:05.000Z", "distro": "noble", "commit": "0280721d6c808991a93dba8168097ee417304b8e", "fileid": "1ba2e3ead1285178bfd8a68fe6fb2f12ec4aa2cd08027f6b14bf98f00104847c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705333179" }, { "r": "4.6.0", "os": "linux", "version": "1.32.0", "date": "2026-05-31T06:33:12.000Z", "distro": "noble", "commit": "0280721d6c808991a93dba8168097ee417304b8e", "fileid": "8ea2a13e102b4c95a3f8e0f531ffac1d1279498670ac037df4969404a3be0399", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705333179" }, { "r": "4.5.3", "os": "mac", "version": "1.32.0", "date": "2026-05-31T06:46:58.000Z", "commit": "0280721d6c808991a93dba8168097ee417304b8e", "fileid": "74654d9c61c4559278b3d11cbe0a8f4ade95db913a762b3b938c45b9600f8554", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705333179" }, { "r": "4.6.0", "os": "mac", "version": "1.32.0", "date": "2026-05-31T06:47:48.000Z", "commit": "0280721d6c808991a93dba8168097ee417304b8e", "fileid": "79b0604c04e87de6553440bddcb7e29a85a81f6fb2227c704d0416418e406a2e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705333179" }, { "r": "4.6.0", "os": "wasm", "version": "1.32.0", "date": "2026-05-31T06:32:02.000Z", "commit": "0280721d6c808991a93dba8168097ee417304b8e", "fileid": "b709caff1c10dfb704947cd498417668388bdc0df953409f5c32f2ca24230f41", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705333179" }, { "r": "4.7.0", "os": "win", "version": "1.32.0", "date": "2026-05-31T06:32:49.000Z", "commit": "0280721d6c808991a93dba8168097ee417304b8e", "fileid": "1e13e4ef4bdfc3582356a514de19bfb522ce5d01544a1502441cd38574e078f5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705333179" }, { "r": "4.5.3", "os": "win", "version": "1.32.0", "date": "2026-05-31T06:31:23.000Z", "commit": "0280721d6c808991a93dba8168097ee417304b8e", "fileid": "0ebb81d9c9a2eb083982832605f866f99b38a7d1535d9593e3aa1420f4d87ae2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705333179" }, { "r": "4.6.0", "os": "win", "version": "1.32.0", "date": "2026-05-31T06:31:21.000Z", "commit": "0280721d6c808991a93dba8168097ee417304b8e", "fileid": "fda97ba31d0226b52f31fbf2f7555670d590126837148060556260ad7811d374", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705333179" } ] }