{ "_id": "6a293685732311cd875a81bb", "Package": "rvarsim", "Title": "R/Bioconductor Variant Simulator with HGVS Notation", "Version": "0.99.1", "Authors@R": "person(\"Liu\", \"Sun\",\nemail = \"sunliu@yxnu.edu.cn\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1459-9478\"))", "Description": "Simulates all possible single nucleotide variants (SNVs)\nacross MANE Select transcripts including coding sequence (CDS),\nuntranslated regions (UTRs), and canonical splice sites.\nOutputs variants in HGVS notation. Provides a comprehensive\nHGVS toolkit: parsing, syntactic and semantic validation,\nnormalization (3' shifting, common affix trimming), format\nconversion (HGVS <-> VCF <-> SPDI), transcription mapping\n(genomic <-> coding), translation to protein consequence,\nbacktranslation from protein to coding variants, variant\nextraction from sequence alignment, and liftover between genome\nassemblies.", "License": "MIT + file LICENSE", "URL": "https://github.com/liu-sun/rvarsim", "BugReports": "https://github.com/liu-sun/rvarsim/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "biocViews": "Genetics, VariantAnnotation, SNP, Sequencing, Transcription,\nVariantDetection, Alignment, Normalization", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-06-10 07:08:19 UTC", "RemoteUrl": "https://github.com/BiocStaging/rvarsim", "RemoteRef": "HEAD", "RemoteSha": "7b0d289dedbea6448b59f9f74ead186b79b02e60", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-10 09:54:23 UTC", "User": "root" }, "Author": "Liu Sun [aut, cre] (ORCID: )", "Maintainer": "Liu Sun ", "MD5sum": "ed5e091ec9ca376eb19ecb659e1a7f9e", "_user": "biocstaging", "_type": "src", "_file": "rvarsim_0.99.1.tar.gz", "_fileid": "0f004edbbfdb6a8ebf0f4c4d9b244cc4dafc9c69aa0270ae4abc2eedab55d257", "_filesize": 189372, "_sha256": "0f004edbbfdb6a8ebf0f4c4d9b244cc4dafc9c69aa0270ae4abc2eedab55d257", "_created": "2026-06-10T09:54:23.000Z", "_published": "2026-06-10T10:03:49.594Z", "_jobs": [ { "job": 80530877058, "time": 303, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7532495451" }, { "job": 80530876928, "time": 496, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7532567601" }, { "job": 80530876904, "time": 447, 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"_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27267925032", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/BiocStaging/rvarsim", "_commit": { "id": "7b0d289dedbea6448b59f9f74ead186b79b02e60", "author": "sunliu ", "committer": "sunliu ", "message": "simulation\n\nvariant simulator\n", "time": 1781075299 }, "_maintainer": { "name": "Liu Sun", "email": "sunliu@yxnu.edu.cn", "login": "liu-sun", "orcid": "0000-0002-1459-9478", "description": "", "uuid": 46041656 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "BiocGenerics", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "BSgenome", "role": "Imports" }, { "package": "ensembldb", 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"Fetch MANE Select transcripts", "topics": [ "fetch_mane_txdb" ] }, { "page": "format_hgvs", "title": "Format variants in HGVS notation", "topics": [ "format_hgvs" ] }, { "page": "generate_variants", "title": "Generate all possible single nucleotide variants", "topics": [ "generate_variants" ] }, { "page": "get_transcript_structure", "title": "Extract transcript structure for variant simulation", "topics": [ "get_transcript_structure" ] }, { "page": "hgvs_conversion", "title": "Convert HGVS to and from other variant formats", "topics": [ "hgvs_conversion" ] }, { "page": "hgvs_to_spdi", "title": "Convert HGVS to SPDI format", "topics": [ "hgvs_to_spdi" ] }, { "page": "hgvs_to_vcf", "title": "Convert HGVS to VCF data.frame", "topics": [ "hgvs_to_vcf" ] }, { "page": "is_valid_hgvs", "title": "Check if an HGVS string is valid (convenience wrapper)", "topics": [ "is_valid_hgvs" ] }, { "page": "liftover_c_hgvs", "title": "Lift over a c. variant by converting to genomic, lifting, then converting back", "topics": [ "liftover_c_hgvs" ] }, { "page": "liftover_hgvs", "title": "Map variants between aligned genomic sequences", "topics": [ "liftover_hgvs" ] }, { "page": "normalize_hgvs", "title": "Normalize HGVS variant descriptions", "topics": [ "normalize_hgvs" ] }, { "page": "parse_hgvs", "title": "Parse HGVS variant descriptions", "topics": [ "parse_hgvs" ] }, { "page": "simulate_variants", "title": "Simulate all possible SNVs for MANE Select transcripts", "topics": [ "simulate_variants" ] }, { "page": "spdi_to_hgvs", "title": "Convert SPDI to HGVS g. notation", "topics": [ "spdi_to_hgvs" ] }, { "page": "transcribe_hgvs", "title": "Map variants between genome and transcript notation", "topics": [ "c_to_g", "g_to_c", "transcribe_hgvs" ] }, { "page": "translate_hgvs", "title": "Infer protein consequences from transcript variants", "topics": [ "translate_hgvs" ] }, { "page": "validate_hgvs", "title": "Validate HGVS variant descriptions", "topics": [ "validate_hgvs" ] }, { "page": "vcf_to_hgvs", "title": "Convert VCF row to HGVS notation", "topics": [ "vcf_to_hgvs" ] } ], "_readme": "https://github.com/BiocStaging/rvarsim/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "ensembldb", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lazyeval", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "ProtGenerics", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", 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