{ "_id": "6a1f0bbbb401979e7341c816", "Package": "RJMCMCNucleosomes", "Version": "1.37.0", "Date": "2025-07-28", "Title": "Bayesian hierarchical model for genome-wide nucleosome\npositioning with high-throughput short-read data (MNase-Seq)", "Description": "This package does nucleosome positioning using informative\nMultinomial-Dirichlet prior in a t-mixture with reversible jump\nestimation of nucleosome positions for genome-wide profiling.", "Authors@R": "c(person(\"Pascal\", \"Belleau\",\nemail=\"pascal_belleau@hotmail.com\", role=c(\"aut\")),\nperson(\"Rawane\", \"Samb\",\nemail=\"rawane.samb.1@ulaval.ca\", role=c(\"aut\")),\nperson(\"Astrid\", \"Deschênes\",\nemail=\"adeschen@hotmail.com\",\nrole=c(\"cre\",\"aut\")),\nperson(\"Khader\", \"Khadraoui\",\nemail=\"Khader.Khadraoui@mat.ulaval.ca\", role=c(\"aut\")),\nperson(\"Lajmi\", \"Lakhal-Chaieb\",\nemail=\"Lajmi.Lakhal@mat.ulaval.ca;\", role=c(\"aut\")),\nperson(\"Arnaud\", \"Droit\",\nemail=\"arnaud.droit@crchuq.ulaval.ca\", role=c(\"aut\")))", "SystemRequirements": "Rcpp", "Encoding": "UTF-8", "License": "Artistic-2.0", "URL": "https://github.com/ArnaudDroitLab/RJMCMCNucleosomes", "BugReports": "https://github.com/ArnaudDroitLab/RJMCMCNucleosomes/issues", "VignetteBuilder": "knitr", "biocViews": "BiologicalQuestion, ChIPSeq, NucleosomePositioning,\nSoftware, StatisticalMethod, Bayesian, Sequencing, Coverage", "RoxygenNote": "6.0.1", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:44:53 UTC", "RemoteUrl": "https://github.com/bioc/RJMCMCNucleosomes", "RemoteRef": "HEAD", "RemoteSha": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-17 09:44:13 UTC", "User": "root" }, "Author": "Pascal Belleau [aut],\nRawane Samb [aut],\nAstrid Deschênes [cre, aut],\nKhader Khadraoui [aut],\nLajmi Lakhal-Chaieb [aut],\nArnaud Droit [aut]", "Maintainer": "Astrid Deschênes ", "MD5sum": "f00d2b7f02c1d785fc14a7f15f48033d", "_user": "bioc", "_type": "src", "_file": "RJMCMCNucleosomes_1.37.0.tar.gz", "_fileid": "8f3b4ff6d80134e23c92e8f6490f3804a58e9914b4a518f89ddaab5986a4026f", "_filesize": 500923, "_sha256": "8f3b4ff6d80134e23c92e8f6490f3804a58e9914b4a518f89ddaab5986a4026f", "_created": "2026-05-17T09:44:13.000Z", "_published": "2026-06-02T16:58:35.101Z", "_jobs": [ { "job": 79126191796, "time": 195, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7041357183" }, { "job": 79126192179, "time": 363, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7041375936" }, { "job": 79126192062, "time": 400, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7041380184" }, { "job": 79126192598, "time": 349, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7041374483" }, { "job": 79126192176, "time": 396, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7041379627" }, { "job": 79126192200, "time": 204, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7041364264" }, { "job": 79126192787, "time": 618, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7041405862" }, { "job": 79126192205, "time": 241, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7041371023" }, { "job": 79126192187, "time": 389, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7041379962" }, { "job": 79126191348, "time": 293, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7041334381" }, { "job": 79126191245, "time": 158, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79126191782, "time": 314, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7041370564" }, { "job": 79126192094, "time": 309, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7041370080" }, { "job": 79126192198, "time": 332, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7041372511" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/RJMCMCNucleosomes", "_commit": { "id": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380293 }, "_maintainer": { "name": "Astrid Deschênes", "email": "adeschen@hotmail.com", "login": "adeschen", "description": "I am a Computational Science Analyst at Cold Spring Harbor Laboratory. ", "uuid": 7254636 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "IRanges", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.5", "role": "Imports" }, { "package": "consensusSeekeR", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.23.10", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "nucleoSim", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-31", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.37.0", "bioc": "3.24" }, { "branch": "release", "version": "1.36.0", "bioc": "3.23" } ], "_topics": [ "biologicalquestion", "chipseq", "nucleosomepositioning", "software", "statisticalmethod", "bayesian", "sequencing", "coverage", "bayesian-t-mixture", "bioconductor", "c-plus-plus", "genome-wide-profiling", "multinomial-dirichlet-prior", "nucleosome-positioning", "nucleosomes", "reversible-jump-mcmc", "gsl", "cpp" ], "_stars": 0, "_contributors": [ { "user": "adeschen", "count": 682, "uuid": 7254636 }, { "user": "belleau", "count": 147, "uuid": 8398253 }, { "user": "rawsamb", "count": 16, "uuid": 6518925 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 368, "source": "https://www.bioconductor.org/packages/stats/bioc/RJMCMCNucleosomes" }, "_devurl": "https://github.com/arnauddroitlab/rjmcmcnucleosomes", "_searchresults": 3, "_rbuild": "4.6.0", "_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/RJMCMCNucleosomes.html", "manual.pdf" ], "_homeurl": "https://github.com/arnauddroitlab/rjmcmcnucleosomes", "_realowner": "bioc", "_cranurl": false, "_exports": [ "mergeAllRDSFilesFromDirectory", "mergeRDSFiles", "plotNucleosomes", "postTreatment", "rjmcmc", "rjmcmcCHR", "segmentation" ], "_datasets": [ { "name": "reads_demo_01", "title": "Forward reads and reverse reads in 'GRanges' format (for demo purpose).", "object": "reads_demo_01", "file": "reads_demo_01.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "reads_demo_02", "title": "Forward reads and reverse reads in 'GRanges' format (for demo purpose).", "object": "reads_demo_02", "file": "reads_demo_02.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "RJMCMC_result", "title": "Nucleosomes obtained by running RJMCMC function using reads from reads_demo_02 dataset (for demo purpose).", "object": "RJMCMC_result", "file": "RJMCMC_result.RData", "class": [ "rjmcmcNucleosomes" ], "fields": [], "table": false, "tojson": false }, { "name": "syntheticNucleosomeReads", "title": "Simulated dataset of reads generated by 'nucleoSim' package (for demo purpose).", "object": "syntheticNucleosomeReads", "file": "syntheticNucleosomeReads.RData", "class": [ "syntheticNucReads" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "RJMCMCNucleosomes-package", "title": "RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)", "topics": [ "RJMCMCNucleosomes-package", "RJMCMCNucleosomes" ] }, { "page": "mergeAllRDSFilesFromDirectory", "title": "Merge nucleosome information from all RDS files present in a same directory. Beware that only nucleosome information from same chromosome should be merged together.", "topics": [ "mergeAllRDSFilesFromDirectory" ] }, { "page": "mergeRDSFiles", "title": "Merge nucleosome information from selected RDS files.", "topics": [ "mergeRDSFiles" ] }, { "page": "plotNucleosomes", "title": "Generate a graph of nucleosome positions with read coverage", "topics": [ "plotNucleosomes" ] }, { "page": "postTreatment", "title": "A post-treatment function to merge closely positioned nucleosomes, from the same chromosome, identified by the 'rjmcmc' function.", "topics": [ "postTreatment" ] }, { "page": "print.rjmcmcNucleosomes", "title": "Formated output of predicted nucleosomes", "topics": [ "print.rjmcmcNucleosomes" ] }, { "page": "print.rjmcmcNucleosomesBeforeAndAfterPostTreatment", "title": "Formated output of predicted nucleosomes", "topics": [ "print.rjmcmcNucleosomesBeforeAndAfterPostTreatment" ] }, { "page": "print.rjmcmcNucleosomesMerge", "title": "Formated output of predicted nucleosomes", "topics": [ "print.rjmcmcNucleosomesMerge" ] }, { "page": "reads_demo_01", "title": "Forward reads and reverse reads in 'GRanges' format (for demo purpose).", "topics": [ "reads_demo_01" ] }, { "page": "reads_demo_02", "title": "Forward reads and reverse reads in 'GRanges' format (for demo purpose).", "topics": [ "reads_demo_02" ] }, { "page": "rjmcmc", "title": "Nucleosome positioning mapping on a segment", "topics": [ "rjmcmc" ] }, { "page": "RJMCMC_result", "title": "Nucleosomes obtained by running RJMCMC function using reads from reads_demo_02 dataset (for demo purpose).", "topics": [ "RJMCMC_result" ] }, { "page": "rjmcmcCHR", "title": "Nucleosome positioning mapping on a large segment, up to a chromosome", "topics": [ "rjmcmcCHR" ] }, { "page": "segmentation", "title": "Split a 'GRanges' containing reads in a list of smaller segments for the 'rjmcmc' function.", "topics": [ "segmentation" ] }, { "page": "syntheticNucleosomeReads", "title": "Simulated dataset of reads generated by 'nucleoSim' package (for demo purpose).", "topics": [ "syntheticNucleosomeReads" ] } ], "_readme": "https://github.com/bioc/RJMCMCNucleosomes/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "cigarillo", "cli", "codetools", "consensusSeekeR", "cpp11", "crayon", "curl", "DelayedArray", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "glue", "httr", "IRanges", "jsonlite", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "mime", "openssl", "R6", "Rcpp", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "vctrs", "XML", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libgsl", "package": "libgsl27", "headers": "libgsl-dev", "source": "gsl", "version": "2.7.1+dfsg-6ubuntu2", "name": "gsl", "homepage": "https://www.gnu.org/software/gsl", "description": "GNU Scientific Library (GSL) -- library package" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "RJMCMCNucleosomes.Rmd", "filename": "RJMCMCNucleosomes.html", "title": "Nucleosome Positioning", "engine": "knitr::rmarkdown", "headings": [ "Licensing and citing", "Introduction", "Loading the RJMCMC package", "RJMCMCNucleosomes analysis", "RJMCMCNucleosomes analysis step by step", "Split the analyzed region into segments", "Run RJMCMCNucleosomes for nucleosome predictions", "Regroup all regions", "Post-process predictions", "Visualisation of the predicted nucleosomes", "RJMCMCNucleosomes analysis of one chromosome in one step", "Session info", "References" ], "created": "2016-12-19 23:27:58", "modified": "2016-12-19 23:27:58", "commits": 1 } ], "_score": 4.6020599913279625, "_indexed": true, "_nocasepkg": "rjmcmcnucleosomes", "_universes": [ "bioc", "adeschen", "arnauddroitlab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.37.0", "date": "2026-05-17T09:48:15.000Z", "distro": "noble", "arch": "aarch64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "1fa2882977092bd9b4ea7144531b4d118110163212f63dd2e8c6f6cdae135d0e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" }, { "r": "4.7.0", "os": "linux", "version": "1.37.0", "date": "2026-05-17T09:48:14.000Z", "distro": "noble", "arch": "x86_64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "9f4623cb691e5c81bfda5846ef3e818ea7fcfb9ebefb92533dfb6bd52df42a6f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" }, { "r": "4.6.0", "os": "linux", "version": "1.37.0", "date": "2026-05-17T09:48:04.000Z", "distro": "noble", "arch": "aarch64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "85d5653230898c879f277dcc1ebea02b8b0a380edd181cdcde9827b2aeb7f088", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" }, { "r": "4.6.0", "os": "linux", "version": "1.37.0", "date": "2026-05-17T09:48:18.000Z", "distro": "noble", "arch": "x86_64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "8be28bc798708405bd6e7a876403898e8c9f06e5f894be3d1329e5c4ceed369d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" }, { "r": "4.5.3", "os": "mac", "version": "1.37.0", "date": "2026-05-17T09:47:22.000Z", "arch": "aarch64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "09aa96b6774e9b9cdd248fadbe953a6b2212d28801996240550224c51060ada8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" }, { "r": "4.5.3", "os": "mac", "version": "1.37.0", "date": "2026-05-17T09:48:52.000Z", "arch": "x86_64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "7756450d94d4c9e9115fa7c84c4ee2b484c7b519edf8a197ecf8c3c0285b0a54", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" }, { "r": "4.6.0", "os": "mac", "version": "1.37.0", "date": "2026-05-17T09:48:00.000Z", "arch": "aarch64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "5a4859b7a03a4c74885634858a10630b9fd643f1825ef874e592a17f297714d7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" }, { "r": "4.6.0", "os": "mac", "version": "1.37.0", "date": "2026-05-17T09:47:29.000Z", "arch": "x86_64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "9b5f04be1d802a9a0d66d8ae306595afb4612cc7945cb5752d63d1e0bb5ca603", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" }, { "r": "4.7.0", "os": "win", "version": "1.37.0", "date": "2026-05-17T09:46:37.000Z", "arch": "x86_64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "c7751102722ef166d2a390b73a9afc139bdaf2161499bb7cefd21134f2baf1d9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" }, { "r": "4.5.3", "os": "win", "version": "1.37.0", "date": "2026-05-17T09:46:32.000Z", "arch": "x86_64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "20e60fa180359d04de0b81cd5794481d4cf925cbae66fa0b262af947c88d3da3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" }, { "r": "4.6.0", "os": "win", "version": "1.37.0", "date": "2026-05-17T09:46:34.000Z", "arch": "x86_64", "commit": "510ac6e62b2118b5d60fe7730dbbc46590ddccfe", "fileid": "c639f26ceb603cd23d2c2929c75963cd5e563d0e81170b72cbe9c060f70d608a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25987345919" } ] }