{ "_id": "6aca154bfe5cc25786e84795", "Package": "leeBamViews", "Title": "leeBamViews -- multiple yeast RNAseq samples excerpted from Lee\n2009", "Version": "1.49.0", "Author": "VJ Carey ", "Description": "data from PMID 19096707; prototype for managing multiple\nNGS samples", "Maintainer": "VJ Carey ", "License": "Artistic 2.0", "LazyLoad": "yes", "biocViews": "ExperimentData, Saccharomyces_cerevisiae_Data,\nSequencingData, RNASeqData, SNPData", "RoxygenNote": "7.1.2", "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 12:23:26 UTC", "RemoteUrl": "https://github.com/bioc/leeBamViews", "RemoteRef": "HEAD", "RemoteSha": "b5c21fdbf00dc8c251c49ece9d8a63f7cfcac551", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 10:30:47 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "leeBamViews_1.49.0.tar.gz", "_fileid": "https://r2.ropensci.org/b8d548d81fea3f01f46d493128b008b36089b72d76d6cf32db8425845cd582ef", "_filesize": 11576935, "_sha256": "b8d548d81fea3f01f46d493128b008b36089b72d76d6cf32db8425845cd582ef", "_expires": "2027-01-18T10:36:56.000Z", "_created": "2026-10-10T10:30:47.000Z", "_published": "2026-10-10T10:36:59.006Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38044902797", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 2, "warning": 2, "note": 9 }, "_upstream": "https://github.com/bioc/leeBamViews", "_commit": { "id": "b5c21fdbf00dc8c251c49ece9d8a63f7cfcac551", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379006 }, "_maintainer": { "name": "VJ Carey", "email": "stvjc@channing.harvard.edu", "login": "vjcitn", "description": "Professor of Medicine, Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School.", "uuid": 4624066 }, "_distro": "resolute", "_jobs": [ { "job": 114193200711, "time": 162, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11667203329" }, { "job": 114193200773, "time": 309, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11667747571" }, { "job": 114193200743, "time": 312, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11667423331" }, { "job": 114192415028, "time": 274, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11667308038" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.15.0", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "Rsamtools", "version": ">= 0.1.50", "role": "Depends" }, { "package": "BSgenome", "role": "Depends" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "GenomicAlignments", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "biomaRt", "role": "Suggests" }, { "package": "org.Sc.sgd.db", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.49.0", "bioc": "3.24", "repository": "data/experiment" }, { "branch": "release", "version": "1.48.0", "bioc": "3.23", "repository": "data/experiment" } ], "_topics": [ "experimentdata", "saccharomyces_cerevisiae_data", "sequencingdata", "rnaseqdata", "snpdata", "datapkg" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 21, "_datapkg": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/leeBamViews.html", "extra/manual.pdf" ], "_cranurl": false, "_exports": [ "tabulateReads", "totalReadCounts" ], "_datasets": [ { "name": "leeRPKM", "title": "supplemental data extract on RNA seq results in yeast", "object": "leeRPKM", "file": "leeRPKM.rda", "class": [ "data.frame" ], "fields": [ "chr", "strand", "start", "end", "name", "feature", "orf_classification", "gene", "wt.reads", "rrp.reads", "ski.reads", "xrn.reads", "wt.rpkm", "rrp.rpkm", "ski.rpkm", "xrn.rpkm" ], "rows": 6291, "table": true, "tojson": true }, { "name": "leeUnn", "title": "supplemental data extracts on existing evidence of transcription in yeast", "object": "leeUnn", "file": "leeUnn.rda", "class": [ "data.frame" ], "fields": [ "chr", "start", "end", "strand", "lengthWithoutMask", "length", "lambda", "background5", "background20", "reads", "study" ], "rows": 54822, "table": true, "tojson": true } ], "_help": [ { "page": "bs1", "title": "BamViews instance construction related to yeast RNA-seq", "topics": [ "bs1" ] }, { "page": "leeRPKM", "title": "supplemental data extract on RNA seq results in yeast", "topics": [ "leeRPKM" ] }, { "page": "leeUnn", "title": "supplemental data extracts on existing evidence of transcription in yeast", "topics": [ "leeUnn" ] }, { "page": "tabulateReads", "title": "tabulate counts of alignments occurring in specified genomic regions", "topics": [ "tabulateReads", "tabulateReads,BamViews,character_OR_NULL,logical,function-method", "tabulateReads,BamViews,character_OR_NULL,missing,missing-method", "tabulateReads,BamViews,missing,missing,missing-method" ] }, { "page": "totalReadCounts", "title": "scan BAM files for total read counts", "topics": [ "totalReadCounts", "totalReadCounts,BamViews-method" ] } ], "_rundeps": [ "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "BSgenome", "cigarillo", "codetools", "cpp11", "crayon", "curl", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "httr", "IRanges", "jsonlite", "lambda.r", "matrixStats", "mime", "openssl", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "Rsamtools", "rtracklayer", "S4Vectors", "Seqinfo", "snow", "sys", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "leeViews.Rnw", "filename": "leeViews.pdf", "title": "managing multiple NGS samples with bamViews", "engine": "utils::Sweave", "headings": [ "Introduction", "Basic design", "Illustration", "Comparative counts in a set of regions of interest", "Larger scale sanity check", "Statistical analyses of differential expression", "Summary", "Session data" ], "created": "2012-03-08 08:07:09", "modified": "2022-01-05 15:47:58", "commits": 7 } ], "_score": 3.623249290397901, "_indexed": true, "_nocasepkg": "leebamviews", "_universes": [ "bioc", "vjcitn" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.49.0", "date": "2026-10-10T10:34:40.000Z", "distro": "resolute", "commit": "b5c21fdbf00dc8c251c49ece9d8a63f7cfcac551", "fileid": "https://r2.ropensci.org/f1b7362eb3daeba0aea545420284a274ae54a55e093502b00ef7d0f71861aecd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38044902797" }, { "r": "4.6.1", "os": "linux", "version": "1.49.0", "date": "2026-10-10T10:34:29.000Z", "distro": "resolute", "commit": "b5c21fdbf00dc8c251c49ece9d8a63f7cfcac551", "fileid": "https://r2.ropensci.org/655727c94ac30c04469db186d4372f008925e107dcefacf6b35da32bdef2f878", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38044902797" } ] }