{ "_id": "6a339f683efcd9bda43a79e0", "Package": "genomicInstability", "Version": "1.18.0", "Date": "2020-02-21", "Title": "Genomic Instability estimation for scRNA-Seq", "Authors@R": "c(person(\"Mariano\", \"Alvarez\", role=c(\"aut\", \"cre\"),\nemail=\"reef103@gmail.com\"),\nperson(\"Pasquale\", \"Laise\", role=\"aut\",\nemail=\"plaise@darwinhealth.com\"),\nperson(\"DarwinHealth\", role=\"cph\"))", "Description": "This package contain functions to run genomic instability\nanalysis (GIA) from scRNA-Seq data. GIA estimates the\nassociation between gene expression and genomic location of the\ncoding genes. It uses the aREA algorithm to quantify the\nenrichment of sets of contiguous genes (loci-blocks) on the\ngene expression profiles and estimates the Genomic Instability\nScore (GIS) for each analyzed cell.", "License": "file LICENSE", "biocViews": "SystemsBiology, GeneExpression, SingleCell", "BiocType": "Software", "URL": "https://github.com/DarwinHealth/genomicInstability", "BugReports": "https://github.com/DarwinHealth/genomicInstability", "Encoding": "UTF-8", "ARoxygenNote": "7.1.1", "RoxygenNote": "7.1.1", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:56:43 UTC", "RemoteUrl": "https://github.com/bioc/genomicInstability", "RemoteRef": "RELEASE_3_23", "RemoteSha": "5df93470d2833edf0865738455a6306ce1bc01af", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-18 07:12:45 UTC", "User": "root" }, "Author": "Mariano Alvarez [aut, cre],\nPasquale Laise [aut],\nDarwinHealth [cph]", "Maintainer": "Mariano Alvarez ", "MD5sum": "f6f1db4ebdf14c279c75e2c566657e22", "_user": "bioc-release", "_type": "src", "_file": "genomicInstability_1.18.0.tar.gz", "_fileid": "4dc3900e8358730e1a54972f58e7f202a4425a9b1e30bddf101c9fce193c6c88", "_filesize": 1242340, "_sha256": "4dc3900e8358730e1a54972f58e7f202a4425a9b1e30bddf101c9fce193c6c88", "_created": "2026-06-18T07:12:45.000Z", "_published": "2026-06-18T07:34:00.254Z", "_jobs": [ { "job": 82074791728, "time": 188, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7716588184" }, { "job": 82074791750, "time": 371, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7716643837" }, { "job": 82074791795, "time": 369, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7716643175" }, { "job": 82074791760, "time": 308, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7716905447" }, { "job": 82074791746, "time": 239, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7716881077" }, { "job": 82074087197, "time": 271, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7716529101" }, { "job": 82074791757, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7716571992" }, { "job": 82074791800, "time": 277, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7716615009" }, { "job": 82074791790, "time": 321, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7716628584" }, { "job": 82074791781, "time": 297, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7716622121" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742871781", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/genomicInstability", "_commit": { "id": "5df93470d2833edf0865738455a6306ce1bc01af", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381003 }, "_maintainer": { "name": "Mariano Alvarez", "email": "reef103@gmail.com", "login": "reef103", "description": "", "uuid": 31012433 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "checkmate", "role": "Depends" }, { "package": "mixtools", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Suggests" }, { "package": "ExperimentHub", "role": "Suggests" }, { "package": "pROC", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23" } ], "_topics": [ "systemsbiology", "geneexpression", "singlecell" ], "_stars": 5, "_contributors": [ { "user": "reef103", "count": 44, "uuid": 31012433 }, { "user": "nturaga", "count": 4, "uuid": 2746443 }, { "user": "copilot", "count": 2, "uuid": 198982749 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/darwinhealth/genomicinstability", "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/genomicInstability.html", "extra/NEWS.html", "extra/NEWS.txt", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/reef103/genomicinstability", "_realowner": "bioc", "_cranurl": false, "_exports": [ "generateChromosomeGeneSet", "genomicInstabilityScore", "giDensityPlot", "giLikelihood", "inferCNV" ], "_datasets": [ { "name": "geneLength", "title": "Average length of human and mouse known genes", "object": "hg38", "file": "hg38.rda", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "geneLength", "title": "Average length of human and mouse known genes", "object": "mm10", "file": "mm10.rda", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "genePosition", "title": "Chromosomal coordinate of human and mouse known genes", "object": "hg38", "file": "hg38.rda", "class": [ "data.frame" ], "fields": [ "Chromosome", "Coordinate" ], "rows": 25221, "table": true, "tojson": true }, { "name": "genePosition", "title": "Chromosomal coordinate of human and mouse known genes", "object": "mm10", "file": "mm10.rda", "class": [ "data.frame" ], "fields": [ "Chromosome", "Coordinate" ], "rows": 24116, "table": true, "tojson": true } ], "_help": [ { "page": "geneLength", "title": "Average length of human and mouse known genes", "topics": [ "geneLength" ] }, { "page": "genePosition", "title": "Chromosomal coordinate of human and mouse known genes", "topics": [ "genePosition" ] }, { "page": "generateChromosomeGeneSet", "title": "Topological gene sets", "topics": [ "generateChromosomeGeneSet" ] }, { "page": "genomicInstabilityScore", "title": "Genomic Instability Analysis", "topics": [ "genomicInstabilityScore" ] }, { "page": "giDensityPlot", "title": "Genomic instability plot", "topics": [ "giDensityPlot" ] }, { "page": "giLikelihood", "title": "Genomic instability likelihood", "topics": [ "giLikelihood" ] }, { "page": "inferCNV", "title": "Inference of CNV from expression data", "topics": [ "inferCNV" ] }, { "page": "plot.inferCNV", "title": "Plot chromosome map", "topics": [ "plot.inferCNV" ] } ], "_rundeps": [ "abind", "askpass", "backports", "base64enc", "Biobase", "BiocGenerics", "bslib", "cachem", "checkmate", "cli", "cpp11", "crosstalk", "curl", "data.table", "DelayedArray", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "IRanges", "isoband", "jquerylib", "jsonlite", "kernlab", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "mixtools", "nlme", "openssl", "otel", "pillar", "pkgconfig", "plotly", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "segmented", "Seqinfo", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XVector", "yaml" ], "_vignettes": [ { "source": "genomicInstability.Rnw", "filename": "genomicInstability.pdf", "title": "Using genomicInstability", "engine": "utils::Sweave", "headings": [ "Overview of genomicInstability", "Installation of genomicInstability package", "Use-case example for the analysis of HNSC and normal cells", "Session Information" ], "created": "2021-02-26 04:08:58", "modified": "2021-03-05 03:10:25", "commits": 7 } ], "_score": 4.301029995663981, "_indexed": false, "_nocasepkg": "genomicinstability", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/genomicInstability", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.18.0", "date": "2026-06-18T07:16:31.000Z", "distro": "noble", "commit": "5df93470d2833edf0865738455a6306ce1bc01af", "fileid": "d50fefe7e795811926ed29a124a0094d44410f1c3f84c1e6d60ceaf6b0c96ff7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742871781" }, { "r": "4.6.0", "os": "linux", "version": "1.18.0", "date": "2026-06-18T07:16:23.000Z", "distro": "noble", "commit": "5df93470d2833edf0865738455a6306ce1bc01af", "fileid": "05a4d2258674f716f744ddeb5865cba946a7036a69711255eb5d8f0ce7af769e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742871781" }, { "r": "4.5.3", "os": "mac", "version": "1.18.0", "date": "2026-06-18T07:30:18.000Z", "commit": "5df93470d2833edf0865738455a6306ce1bc01af", "fileid": "91d7c278a6d2f1031fdcd1f0de7bc09d2f439ffefbe3ab167f1bfbc80dcf70fe", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742871781" }, { "r": "4.6.0", "os": "mac", "version": "1.18.0", "date": "2026-06-18T07:29:43.000Z", "commit": "5df93470d2833edf0865738455a6306ce1bc01af", "fileid": "7faef65900c18d425295c0f550d80b1ecab9db3f2555fb29bfae92445683b5ec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742871781" }, { "r": "4.6.0", "os": "wasm", "version": "1.18.0", "date": "2026-06-18T07:15:30.000Z", "commit": "5df93470d2833edf0865738455a6306ce1bc01af", "fileid": "7ee446b38a69f2068bac95a1d4dace7d93af65013f0636b9125e57a2e60b959c", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742871781" }, { "r": "4.7.0", "os": "win", "version": "1.18.0", "date": "2026-06-18T07:14:16.000Z", "commit": "5df93470d2833edf0865738455a6306ce1bc01af", "fileid": "be65f08fea94467de2b583351ec4f7be349f6a3e93b3e3fd43d08f2c9aa5df34", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742871781" }, { "r": "4.5.3", "os": "win", "version": "1.18.0", "date": "2026-06-18T07:14:56.000Z", "commit": "5df93470d2833edf0865738455a6306ce1bc01af", "fileid": "840a9d35c908749ca8873fad4fa95b6b93476c9b8d47d444c4805a2cc69f714b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742871781" }, { "r": "4.6.0", "os": "win", "version": "1.18.0", "date": "2026-06-18T07:14:43.000Z", "commit": "5df93470d2833edf0865738455a6306ce1bc01af", "fileid": "d8c5eeed5699af8cad386d4995f11d52a5ef20b8b151e095434e325e1ed3f70f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742871781" } ] }