{ "_id": "6a34e7af3efcd9bda43ccb61", "Package": "RSVSim", "Type": "Package", "Title": "RSVSim: an R/Bioconductor package for the simulation of\nstructural variations", "Version": "1.53.0", "Date": "2024-04-23", "Author": "Christoph Bartenhagen", "Maintainer": "Christoph Bartenhagen ", "Description": "RSVSim is a package for the simulation of deletions,\ninsertions, inversion, tandem-duplications and translocations\nof various sizes in any genome available as FASTA-file or\nBSgenome data package. SV breakpoints can be placed uniformly\naccross the whole genome, with a bias towards repeat regions\nand regions of high homology (for hg19) or at user-supplied\ncoordinates.", "License": "LGPL-3", "biocViews": "Sequencing", "Config/pak/sysreqs": "libbz2-dev libjpeg-dev liblzma-dev libpng-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:37:10 UTC", "RemoteUrl": "https://github.com/bioc/RSVSim", "RemoteRef": "HEAD", "RemoteSha": "9485f7ccd96fa3654681446b48f14c711e2fe5fc", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-19 06:46:46 UTC", "User": "root" }, "MD5sum": "2c498c4b4cdd08de40b072cfc068614a", "_user": "bioc", "_type": "src", "_file": "RSVSim_1.53.0.tar.gz", "_fileid": "6f35e3235931565338b523e49a5810bfea10349357d8d0fb68b2fd5d4d071ee4", "_filesize": 641749, "_sha256": "6f35e3235931565338b523e49a5810bfea10349357d8d0fb68b2fd5d4d071ee4", "_created": "2026-06-19T06:46:46.000Z", "_published": "2026-06-19T06:54:39.022Z", "_jobs": [ { "job": 82298691530, "time": 262, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7743477138" }, { "job": 82298691543, "time": 418, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7743516074" }, { "job": 82298691573, "time": 417, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7743515594" }, { "job": 82298691557, "time": 255, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7743475126" }, { "job": 82298691545, "time": 276, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7743480051" }, { "job": 82298034272, "time": 324, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7743412601" }, { "job": 82298691541, "time": 204, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7743462932" }, { "job": 82298691592, "time": 375, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7743505219" }, { "job": 82298691558, "time": 369, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7743503680" }, { "job": 82298691566, "time": 407, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7743513444" } ], "_bioccheck": { "error": 2, "warning": 4, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27755819112", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/RSVSim", "_commit": { "id": "9485f7ccd96fa3654681446b48f14c711e2fe5fc", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379830 }, "_maintainer": { "name": "Christoph Bartenhagen", "email": "c.bartenhagen@uni-koeln.de", "login": "seismicon", "description": "", "uuid": 79155204 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Biostrings", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "ShortRead", "role": "Imports" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19.masked", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "rtracklayer", "role": "Suggests" }, { "package": "pwalign", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.53.0", "bioc": "3.24" }, { "branch": "release", "version": "1.52.0", "bioc": "3.23" } ], "_topics": [ "sequencing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 13, "_searchresults": 19, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/RSVSim.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "compareSV", "estimateSVSizes", "simulateSV" ], "_datasets": [ { "name": "segDups", "title": "Segmental duplications", "object": "segmentalDuplications", "file": "segmentalDuplications.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "weightsMechanisms", "title": "Weights for SV formation mechanisms", "object": "weightsMechanisms", "file": "weightsMechanisms.RData", "class": [ "data.frame" ], "fields": [ "dels", "ins", "invs", "dups", "trans" ], "rows": 5, "table": true, "tojson": true }, { "name": "weightsRepeats", "title": "Weights for repeat region bias", "object": "weightsRepeats", "file": "weightsRepeats.RData", "class": [ "data.frame" ], "fields": [ "NAHR", "NHR", "TEI", "VNTR", "Other" ], "rows": 7, "table": true, "tojson": true } ], "_help": [ { "page": "compareSVs", "title": "Compare the simulation with a set of SVs", "topics": [ "compareSV", "compareSV,character,character-method", "compareSV,character,data.frame-method", "compareSV,data.frame,data.frame-method" ] }, { "page": "estimateSVSizes", "title": "Draw random structural variation sizes from a beta distribution", "topics": [ "estimateSVSizes", "estimateSVSizes,numeric,missing,ANY,ANY,character-method", "estimateSVSizes,numeric,missing,ANY,ANY,missing-method", "estimateSVSizes,numeric,numeric,ANY,ANY,missing-method" ] }, { "page": "segmentalDuplications", "title": "Segmental duplications", "topics": [ "segDups" ] }, { "page": "simulateSV", "title": "Structural Variant Simulation", "topics": [ "simulateSV", "simulateSV,ANY", "simulateSV,ANY-method" ] }, { "page": "weightsMechanisms", "title": "Weights for SV formation mechanisms", "topics": [ "weightsMechanisms" ] }, { "page": "weightsRepeats", "title": "Weights for repeat region bias", "topics": [ "weightsRepeats" ] } ], "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bitops", "cigarillo", "codetools", "cpp11", "crayon", "DelayedArray", "deldir", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "hwriter", "interp", "IRanges", "jpeg", "lambda.r", "lattice", "latticeExtra", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "png", "pwalign", "RColorBrewer", "Rcpp", "RcppEigen", "Rhtslib", "Rsamtools", "S4Arrays", "S4Vectors", "Seqinfo", "ShortRead", "snow", "SparseArray", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "vignette.Rnw", "filename": "vignette.pdf", "title": "RSVSim: an R/Bioconductor package for the simulation of structural variations", "engine": "utils::Sweave", "headings": [ "Introduction", "Structural variation simulation", "Simulation of biases towards SV formation mechanisms and repeat regions", "Simulation of additional breakpoint mutations", "Simulation within a genome subset", "Comparing two sets of SVs", "Setting structural variation sizes", "Runtime", "Session Information" ], "created": "2013-11-01 20:28:14", "modified": "2015-05-03 19:54:03", "commits": 2 } ], "_score": 4.57978359661681, "_indexed": true, "_nocasepkg": "rsvsim", "_universes": [ "bioc", "seismicon" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.53.0", "date": "2026-06-19T06:51:41.000Z", "distro": "noble", "commit": "9485f7ccd96fa3654681446b48f14c711e2fe5fc", "fileid": "0d9fc1aedf2de5f968d64709de3c2b327b50c04d3b341eec2ae0d082dc229dfa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755819112" }, { "r": "4.6.0", "os": "linux", "version": "1.53.0", "date": "2026-06-19T06:51:40.000Z", "distro": "noble", "commit": "9485f7ccd96fa3654681446b48f14c711e2fe5fc", "fileid": "2fff91ff6bbe62a34669bbab8b54c7f06e38dceb57a8eca87b0ea1049f970bef", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755819112" }, { "r": "4.5.3", "os": "mac", "version": "1.53.0", "date": "2026-06-19T06:49:52.000Z", "commit": "9485f7ccd96fa3654681446b48f14c711e2fe5fc", "fileid": "7b63dba2455e98c8be4dd46313f639f7a5cdedeffdf098ecfc57a7c15829e621", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755819112" }, { "r": "4.6.0", "os": "mac", "version": "1.53.0", "date": "2026-06-19T06:50:00.000Z", "commit": "9485f7ccd96fa3654681446b48f14c711e2fe5fc", "fileid": "3acf7f2a0774978381fc5440205fff7ef538dc22e7d7937c081f727a1ff14a06", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755819112" }, { "r": "4.6.0", "os": "wasm", "version": "1.53.0", "date": "2026-06-19T06:50:43.000Z", "commit": "9485f7ccd96fa3654681446b48f14c711e2fe5fc", "fileid": "ff05d66f4fefed0e200e76377bac68b74f9b482e56336a68be9cceacb32539aa", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755819112" }, { "r": "4.7.0", "os": "win", "version": "1.53.0", "date": "2026-06-19T06:50:33.000Z", "commit": "9485f7ccd96fa3654681446b48f14c711e2fe5fc", "fileid": "ede7e176b13799bf6726dbce74ef6a6d5546e6f73bbb8b2bf016e90a07f95870", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755819112" }, { "r": "4.5.3", "os": "win", "version": "1.53.0", "date": "2026-06-19T06:50:37.000Z", "commit": "9485f7ccd96fa3654681446b48f14c711e2fe5fc", "fileid": "d236dbfcf42d21642200e6bf8d841f568d2ec84f899f206c46ede80a8764f5cb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755819112" }, { "r": "4.6.0", "os": "win", "version": "1.53.0", "date": "2026-06-19T06:50:44.000Z", "commit": "9485f7ccd96fa3654681446b48f14c711e2fe5fc", "fileid": "5b58fd4cf20c8481eca82ab1c8ffabf2505439bc179e578eea14755307dea252", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755819112" } ] }