{ "_id": "6aca1872fe5cc25786e84a1d", "Package": "NanoporeRNASeq", "Type": "Package", "Title": "Nanopore RNA-Seq Example data", "Version": "1.23.1", "Authors@R": "c(person(\"Jonathan\", \"Goeke\", role = \"aut\",\nemail = \"Jonathan_GOEKE@a-star.edu.sg\"),\nperson(\"Ying\", \"Chen\", role = \"cre\",\nemail = \"chen_ying@gis.a-star.edu.sg\"),\nperson(\"Yuk Kei\",\"Wan\", role = \"aut\",\nemail = \"yukkeiwan622@gmail.com\"))", "Description": "The NanoporeRNASeq package contains long read RNA-Seq data\ngenerated using Oxford Nanopore Sequencing. The data consists\nof 6 samples from two human cell lines (K562 and MCF7) that\nwere generated by the SG-NEx project. Each of these cell lines\nhas three replicates, with 1 direct RNA sequencing data and 2\ncDNA sequencing data. Reads are aligned to chromosome 22\n(Grch38) and stored as bam files. The original data is from the\nSG-NEx project.", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "SystemRequirements": "", "biocViews": "ExperimentHub, ExperimentData, RNASeqData, Genome,\nSequencingData", "bugReports": "https://github.com/GoekeLab/NanoporeRNASeq/issues", "URL": "https://github.com/GoekeLab/NanoporeRNASeq", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-01 09:48:47 UTC", "RemoteUrl": "https://github.com/bioc/NanoporeRNASeq", "RemoteRef": "HEAD", "RemoteSha": "5994e53262d5c5c0f57dff77778a2e29233d1b91", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 10:44:37 UTC", "User": "root" }, "Author": "Jonathan Goeke [aut],\nYing Chen [cre],\nYuk Kei Wan [aut]", "Maintainer": "Ying Chen ", "_user": "bioc", "_type": "src", "_file": "NanoporeRNASeq_1.23.1.tar.gz", "_fileid": "https://r2.ropensci.org/2018a3265d20dfa3cb51331b98ef467df4ff13de4636b7f92cde436563080f73", "_filesize": 201442, "_sha256": "2018a3265d20dfa3cb51331b98ef467df4ff13de4636b7f92cde436563080f73", "_expires": "2027-01-18T10:50:24.000Z", "_created": "2026-10-10T10:44:37.000Z", "_published": "2026-10-10T10:50:26.302Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38045586331", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 1, "note": 5 }, "_upstream": "https://github.com/bioc/NanoporeRNASeq", "_commit": { "id": "5994e53262d5c5c0f57dff77778a2e29233d1b91", "author": "Chen Ying ", "committer": "Chen Ying ", "message": "version bump and bug fix\n", "time": 1790848127 }, "_maintainer": { "name": "Ying Chen", "email": "chen_ying@gis.a-star.edu.sg" }, "_distro": "resolute", "_jobs": [ { "job": 114195508356, "time": 191, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11667743966" }, { "job": 114195508439, "time": 305, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11667149981" }, { "job": 114195508447, "time": 294, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11666843945" }, { "job": 114194393501, "time": 391, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11667169371" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "ExperimentHub", "version": ">= 1.15.3", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "bambu", "role": "Suggests" }, { "package": "ggbio", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.NCBI.GRCh38", "role": "Suggests" }, { "package": "circlize", "role": "Suggests" }, { "package": "ComplexHeatmap", "role": "Suggests" }, { "package": "apeglm", "role": "Suggests" }, { "package": "rlang", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "GenomicAlignments", "role": "Suggests" }, { "package": "Rsamtools", "role": "Suggests" }, { "package": "parallel", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-40", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.1", "bioc": "3.24", "repository": "data/experiment" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23", "repository": "data/experiment" } ], "_topics": [ "experimenthub", "experimentdata", "rnaseqdata", "genome", "sequencingdata", "bioconductor", "long-reads", "nanopore", "rna-seq", "sg-nex", "datapkg" ], "_stars": 9, "_contributors": [ { "user": "yuukiiwa", "count": 93, "uuid": 41866052 }, { "user": "hpages", "count": 12, "uuid": 8810451 }, { "user": "lshep", "count": 8, "uuid": 18724380 }, { "user": "cying111", "count": 4, "uuid": 25293260 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/goekelab/nanoporernaseq", "_searchresults": 7, "_datapkg": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NanoporeRNASeq.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_exports": [], "_datasets": [ { "name": "HsChr22BambuAnnotation", "title": "BambuAnnotation of the first half of Human Sapiens Chr22", "object": "HsChr22BambuAnnotation", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "SGNexSamples", "title": "SG-Nex samples from Nanopore RNA-Seq", "object": "SGNexSamples", "class": [ "DFrame" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "HsChr22BambuAnnotation", "title": "BambuAnnotation of the first half of Human Sapiens Chr22", "topics": [ "HsChr22BambuAnnotation" ] }, { "page": "NanoporeRNASeq", "title": "NanoporeRNASeq package with long-read RNA sequencing data", "topics": [ "NanoporeRNASeq" ] }, { "page": "SGNexSamples", "title": "SG-Nex samples from Nanopore RNA-Seq", "topics": [ "SGNexSamples" ] } ], "_readme": "https://github.com/bioc/NanoporeRNASeq/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "AnnotationHub", "askpass", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "dbplyr", "dplyr", "ExperimentHub", "fastmap", "filelock", "generics", "glue", "httr", "httr2", "IRanges", "jsonlite", "KEGGREST", "lifecycle", "magrittr", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "purrr", "R6", "rappdirs", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector", "yaml" ], "_vignettes": [ { "source": "NanoporeRNASeq.Rmd", "filename": "NanoporeRNASeq.html", "title": "An introduction to the bambu package using NanoporeRNASeq data", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Accessing NanoporeRNASeq data", "Load the NanoporeRNASeq package", "List the samples", "List the available BamFile", "Get the annotation GRangesList", "Visualizing gene of interest from a single bam file", "Running Bambu with NanoporeRNASeq data", "Load the bambu package", "Run bambu", "Visualizing gene examples" ], "created": "2020-05-22 06:43:04", "modified": "2026-10-01 09:23:00", "commits": 20 } ], "_score": 5.2552725051033065, "_indexed": true, "_nocasepkg": "nanoporernaseq", "_universes": [ "bioc", "goekelab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.1", "date": "2026-10-10T10:49:30.000Z", "distro": "resolute", "commit": "5994e53262d5c5c0f57dff77778a2e29233d1b91", "fileid": "https://r2.ropensci.org/a1368dd8e488649e5171125e7c2b4eec5547f9dd638a7fb8f7a1793080fe96f1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38045586331" }, { "r": "4.6.1", "os": "linux", "version": "1.23.1", "date": "2026-10-10T10:49:21.000Z", "distro": "resolute", "commit": "5994e53262d5c5c0f57dff77778a2e29233d1b91", "fileid": "https://r2.ropensci.org/f946158ece49f839a17ddfab5fa1c840f81b12c9e2b94a12d927cc34a62a1a6a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38045586331" } ] }