{ "_id": "6a198025acfb0bcc41df87ca", "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", "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "biocViews": "ImmunoOncology, StatisticalMethod, WholeGenome, ExomeSeq", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "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": "2026-04-28 12:42:52 UTC", "RemoteUrl": "https://github.com/bioc/Uniquorn", "RemoteRef": "HEAD", "RemoteSha": "f9ade8c55523a15a4074b843c7f2df3e6a051803", "Packaged": { "Date": "2026-05-29 10:10:11 UTC", "User": "root" }, "Maintainer": "Raik Otto ", "MD5sum": "1cea55701900861bcd7681012be72385", "_user": "bioc", "_type": "src", "_file": "Uniquorn_2.33.0.tar.gz", "_fileid": "1cd94cf3aa25e09234129b1f7e0680688e036a46f8c6911b90888c207de01429", "_filesize": 2470463, "_sha256": "1cd94cf3aa25e09234129b1f7e0680688e036a46f8c6911b90888c207de01429", "_created": "2026-05-29T10:10:11.000Z", "_published": "2026-05-29T12:01:41.366Z", "_jobs": [ { "job": 78480907526, "time": 198, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7288326821" }, { "job": 78480907664, "time": 390, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7288381748" }, { "job": 78480907654, "time": 421, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7288390778" }, { "job": 78480907681, "time": 225, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7290149094" }, { "job": 78480907569, "time": 195, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7290111620" }, { "job": 78480279341, "time": 260, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7288267805" }, { "job": 78480907543, "time": 161, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7288315462" }, { "job": 78480907600, "time": 331, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7288365517" }, { "job": 78480907629, "time": 317, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7288361516" }, { "job": 78480907683, "time": 284, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7288351768" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26631207411", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Uniquorn", "_commit": { "id": "f9ade8c55523a15a4074b843c7f2df3e6a051803", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380172 }, "_maintainer": { "name": "Raik Otto", "email": "raik.otto@hu-berlin.de", "login": "raikotto", "description": "Bioinformatician with specialisation in Machine-Learning ", "uuid": 1502739 }, "_distro": "noble", "_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": "2025-33", "n": 1 }, { "week": "2025-43", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.33.0", "bioc": "3.24" }, { "branch": "release", "version": "2.32.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "statisticalmethod", "wholegenome", "exomeseq" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 444, "source": "https://www.bioconductor.org/packages/stats/bioc/Uniquorn" }, "_mentions": 2, "_searchresults": 0, "_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/Uniquorn.html", "manual.pdf" ], "_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": "2026-05-29T10:13:36.000Z", "distro": "noble", "commit": "f9ade8c55523a15a4074b843c7f2df3e6a051803", "fileid": "35919054418152dc8a321c1ae8ff0fcec0b6c272fdc06eef8097909dfdf0d47a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631207411" }, { "r": "4.6.0", "os": "linux", "version": "2.33.0", "date": "2026-05-29T10:14:15.000Z", "distro": "noble", "commit": "f9ade8c55523a15a4074b843c7f2df3e6a051803", "fileid": "4c404f6acf6f86af7f6b9c8b414df7c28d2bb6a601bb267fd390737b7f14904f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631207411" }, { "r": "4.5.3", "os": "mac", "version": "2.33.0", "date": "2026-05-29T11:58:53.000Z", "commit": "f9ade8c55523a15a4074b843c7f2df3e6a051803", "fileid": "88e862a90bc1dd70423e108ee640202b73b2132c6ccd4b75bade7d1d2db6f019", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631207411" }, { "r": "4.6.0", "os": "mac", "version": "2.33.0", "date": "2026-05-29T11:56:56.000Z", "commit": "f9ade8c55523a15a4074b843c7f2df3e6a051803", "fileid": "287b9cc77f01b88d3a3999fd8902636f6ccb187d6515ee6a7c995a63102f78a6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631207411" }, { "r": "4.6.0", "os": "wasm", "version": "2.33.0", "date": "2026-05-29T10:13:33.000Z", "commit": "f9ade8c55523a15a4074b843c7f2df3e6a051803", "fileid": "459575a81f26a69462a114ed37cf551272e648a08f6b24ecba6fe42d8f3de5e7", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631207411" }, { "r": "4.7.0", "os": "win", "version": "2.33.0", "date": "2026-05-29T10:12:26.000Z", "commit": "f9ade8c55523a15a4074b843c7f2df3e6a051803", "fileid": "47a31a5e79395d5f53613119cd74dd1a370c07e2af7b173970531a120529c127", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631207411" }, { "r": "4.5.3", "os": "win", "version": "2.33.0", "date": "2026-05-29T10:12:19.000Z", "commit": "f9ade8c55523a15a4074b843c7f2df3e6a051803", "fileid": "52215c414fe92a9ee5cfd5545ccecde45552607258c71f7a7745844b656e9d10", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631207411" }, { "r": "4.6.0", "os": "win", "version": "2.33.0", "date": "2026-05-29T10:12:44.000Z", "commit": "f9ade8c55523a15a4074b843c7f2df3e6a051803", "fileid": "7adc126552ee3781b42d6180cbcccbb247dca155af3382353a0948bb4124f273", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631207411" } ] }