{ "_id": "6adb13ad7e19ec392c1cc803", "Package": "Uniquorn", "Title": "Identification of cancer cell lines based on their weighted\nmutational/ variational fingerprint", "Version": "2.33.0", "Authors@R": "person(\"Raik\", \"Otto\", email = \"raik.otto@hu-berlin.de\", role = c(\"aut\", \"cre\"))", "Description": "'Uniquorn' enables users to identify cancer cell lines.\nCancer cell line misidentification and cross-contamination\nreprents a significant challenge for cancer researchers. The\nidentification is vital and in the frame of this package based\non the locations/ loci of somatic and germline mutations/\nvariations. The input format is vcf/ vcf.gz and the files have\nto contain a single cancer cell line sample (i.e. a single\nmember/genotype/gt column in the vcf file).", "License": "Artistic-2.0", "Type": "Package", "Date": "2025-10-22", "Author": "Raik Otto", "NeedsCompilation": "no", "biocViews": "ImmunoOncology, StatisticalMethod, WholeGenome, ExomeSeq", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev perl xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-07 09:42:23 UTC", "RemoteUrl": "https://github.com/bioc/Uniquorn", "RemoteRef": "HEAD", "RemoteSha": "fb579a9afdef98dd38a83c34e1d04bf535bcb4be", "Packaged": { "Date": "2026-10-23 07:49:44 UTC", "User": "root" }, "Maintainer": "Raik Otto ", "_user": "bioc", "_type": "src", "_file": "Uniquorn_2.33.0.tar.gz", "_fileid": "https://r2.ropensci.org/e5e6cf68c44461aa51b2c4290edc741fa7d70e7b5a089d553a296ea526e64973", "_filesize": 2474971, "_sha256": "e5e6cf68c44461aa51b2c4290edc741fa7d70e7b5a089d553a296ea526e64973", "_expires": "2027-01-31T07:58:33.000Z", "_created": "2026-10-23T07:49:44.000Z", "_published": "2026-10-23T07:58:37.740Z", "_upstream": "https://github.com/bioc/Uniquorn", "_status": "success", "_maintainer": { "name": "Raik Otto", "email": "raik.otto@hu-berlin.de", "login": "raikotto", "description": "Bioinformatician with specialisation in Machine-Learning ", "uuid": 1502739 }, "_jobs": [ { "job": 120304208278, "time": 223, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "12486214107" }, { "job": 120304208263, "time": 392, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12487481432" }, { "job": 120304208270, "time": 460, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12487945026" }, { "job": 120304208267, "time": 288, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "12487227244" }, { "job": 120304208392, "time": 309, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12487425988" }, { "job": 120302027457, "time": 355, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12486683732" }, { "job": 120304208338, "time": 159, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12487286675" }, { "job": 120304208658, "time": 321, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12487366968" }, { "job": 120304208402, "time": 311, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12486173159" }, { "job": 120304208329, "time": 242, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12486927444" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39919767130", "_commit": { "id": "fb579a9afdef98dd38a83c34e1d04bf535bcb4be", "author": "Raik Otto ", "committer": "Raik Otto ", "message": "redocumented package with roxygen2 1.8.0\n", "time": 1791366143 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "stringr", "role": "Imports" }, { "package": "R.utils", "role": "Imports" }, { "package": "WriteXLS", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "VariantAnnotation", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-43", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-41", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.33.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "2.32.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "immunooncology", "statisticalmethod", "wholegenome", "exomeseq" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 614, "source": "https://www.bioconductor.org/packages/stats/bioc/Uniquorn" }, "_mentions": 2, "_searchresults": 5, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/Uniquorn.html" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "add_custom_vcf_to_database", "identify_vcf_file", "initiate_canonical_databases", "read_library_names", "remove_ccls_from_database", "remove_library_from_database", "show_contained_ccls", "show_contained_variants_for_ccl", "show_contained_variants_in_library", "show_which_ccls_contain_variant" ], "_help": [ { "page": "add_custom_vcf_to_database", "title": "add_custom_vcf_to_database This function adds the variants of parsed custom CCLs to a monet DB instance", "topics": [ "add_custom_vcf_to_database" ] }, { "page": "add_missing_cls", "title": "add_missing_cls", "topics": [ "add_missing_cls" ] }, { "page": "add_p_q_values_statistics", "title": "add_p_q_values_statistics", "topics": [ "add_p_q_values_statistics" ] }, { "page": "add_penalty_statistics", "title": "add_penalty_statistics", "topics": [ "add_penalty_statistics" ] }, { "page": "create_bed_file", "title": "create_bed_file", "topics": [ "create_bed_file" ] }, { "page": "identify_vcf_file", "title": "identify_VCF_file", "topics": [ "identify_vcf_file" ] }, { "page": "init_and_load_identification", "title": "init_and_load_identification", "topics": [ "init_and_load_identification" ] }, { "page": "initiate_canonical_databases", "title": "initiate_canonical_databases", "topics": [ "initiate_canonical_databases" ] }, { "page": "match_query_ccl_to_database", "title": "match_query_ccl_to_database", "topics": [ "match_query_ccl_to_database" ] }, { "page": "parse_vcf_file", "title": "Filter Parsed VCF Files", "topics": [ "parse_vcf_file" ] }, { "page": "parse_vcf_query_into_db", "title": "parse_vcf_query_into_db This function adds the variants of parsed custom CCLs to a monet DB instance", "topics": [ "parse_vcf_query_into_db" ] }, { "page": "read_library_names", "title": "Library Name Reader", "topics": [ "read_library_names" ] }, { "page": "read_mutation_grange_objects", "title": "read_mutation_grange_objects", "topics": [ "read_mutation_grange_objects" ] }, { "page": "remove_ccls_from_database", "title": "Remove Cancer Cell Line", "topics": [ "remove_ccls_from_database" ] }, { "page": "remove_library_from_database", "title": "Remove entire Library from Database", "topics": [ "remove_library_from_database" ] }, { "page": "show_contained_ccls", "title": "show_contained_ccls", "topics": [ "show_contained_ccls" ] }, { "page": "show_contained_variants_for_ccl", "title": "Variants In Cancer Cell Line", "topics": [ "show_contained_variants_for_ccl" ] }, { "page": "show_contained_variants_in_library", "title": "All variants contained in reference library", "topics": [ "show_contained_variants_in_library" ] }, { "page": "show_which_ccls_contain_variant", "title": "Cancer cell lines with specific variant", "topics": [ "show_which_ccls_contain_variant" ] } ], "_readme": "https://github.com/bioc/Uniquorn/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "doParallel", "fastmap", "foreach", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "httr", "IRanges", "iterators", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "R.methodsS3", "R.oo", "R.utils", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "VariantAnnotation", "vctrs", "WriteXLS", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "Uniquorn.Rmd", "filename": "Uniquorn.html", "title": "Uniquorn vignette", "author": "Raik Otto", "engine": "knitr::rmarkdown", "headings": [ "1 How to make it work: Quickstart", "Installing the Uniquorn", "Test run", "Addition", "Demonstration of the impact of data heterogeneity and incompleteness", "Explanation test data", "2 Add CCLE and CoSMIC CLP CL data", "Current release (CCLE: DepMap Public 22Q1; COSMIC: v95)", "Older releases", "3 Add training CL samples & utility functions", "BED files and Broad Institute IGV visualization" ], "created": "2016-01-27 18:17:05", "modified": "2022-10-14 10:39:17", "commits": 12 } ], "_score": 4.6020599913279625, "_indexed": true, "_nocasepkg": "uniquorn", "_universes": [ "bioc", "raikotto" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.33.0", "date": "2026-10-23T07:53:19.000Z", "distro": "resolute", "commit": "fb579a9afdef98dd38a83c34e1d04bf535bcb4be", "fileid": "https://r2.ropensci.org/edbab47fb4ec3cbda35bc852e48298d7a62d472c671fd31298d6a5a7795a2989", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39919767130" }, { "r": "4.6.1", "os": "linux", "version": "2.33.0", "date": "2026-10-23T07:54:15.000Z", "distro": "resolute", "commit": "fb579a9afdef98dd38a83c34e1d04bf535bcb4be", "fileid": "https://r2.ropensci.org/2fb0fb9980f45574898cdbfa052734cf04fe8d054250e3a78f51a2e28474f384", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39919767130" }, { "r": "4.5.3", "os": "mac", "version": "2.33.0", "date": "2026-10-23T07:52:02.000Z", "commit": "fb579a9afdef98dd38a83c34e1d04bf535bcb4be", "fileid": "https://r2.ropensci.org/0d44cfd3c83aa3eefadf25bb3130284e4d73bd9c1f62392adae58497485e92d2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39919767130" }, { "r": "4.6.1", "os": "mac", "version": "2.33.0", "date": "2026-10-23T07:52:07.000Z", "commit": "fb579a9afdef98dd38a83c34e1d04bf535bcb4be", "fileid": "https://r2.ropensci.org/ae0e522b9175240fbaa9a75995e6818113c9e87f899e12bb3c4bb947dd68e18c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39919767130" }, { "r": "4.6.0", "os": "wasm", "version": "2.33.0", "date": "2026-10-23T07:52:52.000Z", "commit": "fb579a9afdef98dd38a83c34e1d04bf535bcb4be", "fileid": "https://r2.ropensci.org/5c216e7a7c674697802486c9cc16e36d30f0d1c6f142c791bfe41c86c2a040ef", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39919767130" }, { "r": "4.7.0", "os": "win", "version": "2.33.0", "date": "2026-10-23T07:51:41.000Z", "commit": "fb579a9afdef98dd38a83c34e1d04bf535bcb4be", "fileid": "https://r2.ropensci.org/aba17c5c92c80327936fcd3bf5ed7a7a3941aef6cdc35e3077390b693a5223cf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39919767130" }, { "r": "4.5.3", "os": "win", "version": "2.33.0", "date": "2026-10-23T07:51:40.000Z", "commit": "fb579a9afdef98dd38a83c34e1d04bf535bcb4be", "fileid": "https://r2.ropensci.org/2e254b6a5973c02cfb2d8cd12b163d88c6a2d86eeeae4ac0fd925dff703687c7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39919767130" }, { "r": "4.6.1", "os": "win", "version": "2.33.0", "date": "2026-10-23T07:51:19.000Z", "commit": "fb579a9afdef98dd38a83c34e1d04bf535bcb4be", "fileid": "https://r2.ropensci.org/597a0d88b7b5743704ca8d0a692b8242b50409bfb2aca5dcd89ce2cbdace1a0d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39919767130" } ] }