{ "_id": "6a1acf3c1d7bb097a09e0522", "Package": "genomicInstability", "Version": "1.19.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:56:43 UTC", "RemoteUrl": "https://github.com/bioc/genomicInstability", "RemoteRef": "HEAD", "RemoteSha": "190734f5482674ffd9bb2c54c99c6d920861058e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:13:11 UTC", "User": "root" }, "Author": "Mariano Alvarez [aut, cre],\nPasquale Laise [aut],\nDarwinHealth [cph]", "Maintainer": "Mariano Alvarez ", "MD5sum": "e8d06eb853d468cd41171690df0b1d78", "_user": "bioc", "_type": "src", "_file": "genomicInstability_1.19.0.tar.gz", "_fileid": "6bc1ab59168debda5786bbd808b6d85acd80a588f57030a24f94282f262c8529", "_filesize": 1240153, "_sha256": "6bc1ab59168debda5786bbd808b6d85acd80a588f57030a24f94282f262c8529", "_created": "2026-05-30T08:13:11.000Z", "_published": "2026-05-30T11:51:24.912Z", "_jobs": [ { "job": 78635842631, "time": 179, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306759929" }, { "job": 78635842637, "time": 334, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306774411" }, { "job": 78635842638, "time": 331, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306774149" }, { "job": 78635842648, "time": 207, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307951921" }, { "job": 78635842630, "time": 401, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307968172" }, { "job": 78635617169, "time": 258, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306742767" }, { "job": 78635842634, "time": 143, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306756313" }, { "job": 78635842647, "time": 292, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306770456" }, { "job": 78635842642, "time": 381, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306778757" }, { "job": 78635842641, "time": 429, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306783172" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678871098", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/genomicInstability", "_commit": { "id": "190734f5482674ffd9bb2c54c99c6d920861058e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following 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": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_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", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 330, "source": "https://www.bioconductor.org/packages/stats/bioc/genomicInstability" }, "_devurl": "https://github.com/darwinhealth/genomicinstability", "_searchresults": 12, "_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", "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": [], "created": "2021-02-26 04:08:58", "modified": "2021-03-05 03:10:25", "commits": 7 } ], "_score": 4.380211241711606, "_indexed": true, "_nocasepkg": "genomicinstability", "_universes": [ "bioc", "reef103", "darwinhealth" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-05-30T08:16:13.000Z", "distro": "noble", "commit": "190734f5482674ffd9bb2c54c99c6d920861058e", "fileid": "1e649840345daa8b0751fc8ea5eced330937f433bb0eac156056ba3a8402c186", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678871098" }, { "r": "4.6.0", "os": "linux", "version": "1.19.0", "date": "2026-05-30T08:16:32.000Z", "distro": "noble", "commit": "190734f5482674ffd9bb2c54c99c6d920861058e", "fileid": "3eaf5e0fb0708d8b96fef463abfdc9a45448a2a31311468c74017d0f814f7bd1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678871098" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-05-30T11:45:37.000Z", "commit": "190734f5482674ffd9bb2c54c99c6d920861058e", "fileid": "6033c430f51877ecd334c60e5a495c317079d0f23aeba8d212a20c826070795b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678871098" }, { "r": "4.6.0", "os": "mac", "version": "1.19.0", "date": "2026-05-30T11:46:18.000Z", "commit": "190734f5482674ffd9bb2c54c99c6d920861058e", "fileid": "c87253aa7e0d1b7e9ebac9b0eca5bae34f6d7321bd344d05e313d7c2605b7370", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678871098" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-05-30T08:16:05.000Z", "commit": "190734f5482674ffd9bb2c54c99c6d920861058e", "fileid": "4eba1de8d64eb695e00569f9a91f469fc1bc137002d63b1a8cb3791583f45417", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678871098" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-05-30T08:14:48.000Z", "commit": "190734f5482674ffd9bb2c54c99c6d920861058e", "fileid": "105e26315551c6147f18ee8849e957e0dc27c51140d96fa6a4a265bb2ed0780f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678871098" }, { "r": "4.5.3", "os": "win", "version": "1.19.0", "date": "2026-05-30T08:16:12.000Z", "commit": "190734f5482674ffd9bb2c54c99c6d920861058e", "fileid": "9a8033d666fdb58f04024c634a618336a2e846366831461b65354011732bdf49", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678871098" }, { "r": "4.6.0", "os": "win", "version": "1.19.0", "date": "2026-05-30T08:14:45.000Z", "commit": "190734f5482674ffd9bb2c54c99c6d920861058e", "fileid": "f29b842f8598da65dfd74b30a16a7402c9fccd1b0b86e2cfbde9a5f61d65e733", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678871098" } ] }