{ "_id": "6a232a9f530b9bc726bceb38", "Package": "RiskyCNV", "Title": "Risk Analysis of Genomic Copy Number Variation", "Version": "0.1.0", "Authors@R": "c(\nperson(\"Ashok\", \"Palaniappan\", email = \"apalania@scbt.sastra.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-2841-9527\")),\nperson(\"Priyanka\", \"Ramesh\",\nrole = \"aut\"),\nperson(\"Ida\", \"Titus\",\nrole = \"aut\"),\nperson(\"Sangeetha\", \"Muthamilselvan\",\nrole = \"aut\"))", "Description": "Provides a complete seven-step workflow for copy number\nvariation (CNV) analysis applicable to any disease or condition\nwhere samples with genomic copy number data is available.\nSupports built-in grading and risk stratification presets for\nseven major cancers (viz. prostate, breast, colorectal, lung,\ncervical, lymphoma, melanoma) based on clinically validated\nsystems including ISUP Grade Groups, Nottingham Grading System,\nDukes staging, IASLC TNM, FIGO, Ann Arbor/Lugano\nclassification, and Breslow depth. Generalizable to other\ndisease types. An automatic mode derives a normalised Risk\nScore from the data using min-max normalisation and adaptive\nbinning. Custom user-defined thresholds are supported for any\nother disease type. Downstream functions for CNV aberration\ndetection, recurrence analysis, gene annotation, CNV matrix\ngeneration, and CNV-RNA expression correlation are disease-type\nagnostic.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "biocViews": "CopyNumberVariation, GenomicVariation, RNASeq", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 19:55:33 UTC", "User": "root" }, "Author": "Ashok Palaniappan [aut, cre] (ORCID:\n), Priyanka Ramesh\n[aut], Ida Titus [aut], Sangeetha Muthamilselvan [aut]", "Maintainer": "Ashok Palaniappan ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-06-05 15:00:17 UTC", "RemoteUrl": "https://github.com/cran/RiskyCNV", "RemoteRef": "HEAD", "RemoteSha": "35b5ea4dbc08605d146fe9732c98c316e5deef60", "MD5sum": "28becd3b0bc77456cb3bf2b77d710243", "_user": "cran", "_type": "src", "_file": "RiskyCNV_0.1.0.tar.gz", "_fileid": 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"author": "Ashok Palaniappan ", "committer": "cran-robot ", "message": "version 0.1.0\n", "time": 1780671617 }, "_maintainer": { "name": "Ashok Palaniappan", "email": "apalania@scbt.sastra.edu", "login": "apalania-lab", "description": "", "uuid": 143518533, "orcid": "0000-0003-2841-9527" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-23", "n": 1 } ], "_tags": [ { "name": "0.1.0", "date": "2026-06-05" } ], "_topics": [ "copynumbervariation", "genomicvariation", "rnaseq" ], "_stars": 0, "_contributors": [ { "user": "apalania-lab", "count": 1, "uuid": 143518533 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RiskyCNV" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/RiskyCNV.html", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2026-06-05" } ], "_exports": [ "aberration", "annotate", "classify_risk", "correlate_with_expr", "create_CNVMatrix", "extract_metadata", "recurrent" ], "_help": [ { "page": "aberration", "title": "Detect Copy Number Aberrations (Gains and Losses)", "topics": [ "aberration" ] }, { "page": "annotate", "title": "Annotate CNV Regions with Gene Symbols", "topics": [ "annotate" ] }, { "page": "classify_risk", "title": "Classify Samples into Risk Categories", "topics": [ "classify_risk" ] }, { "page": "correlate_with_expr", "title": "Correlate CNV Profiles with Gene Expression Data", "topics": [ "correlate_with_expr" ] }, { "page": "create_CNVMatrix", "title": "Create a CNV Expression Matrix", "topics": [ "create_CNVMatrix" ] }, { "page": "extract_metadata", "title": "Extract Sample Metadata and Classify into Grade or Stage Groups", "topics": [ "extract_metadata" ] }, { "page": "recurrent", "title": "Identify Recurrent Copy Number Variations by Risk Group", "topics": [ "recurrent" ] }, { "page": "RiskyCNV", "title": "RiskyCNV: A General-Purpose CNV Analysis Workflow for Disease Risk Stratification", "topics": [ "RiskyCNV-package", "RiskyCNV" ] } ], "_rundeps": [ "BiocGenerics", "cli", 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