{ "_id": "6a17ee22acfb0bcc41da53e0", "Package": "OmicsQC", "Type": "Package", "Title": "Nominating Quality Control Outliers in Genomic Profiling Studies", "Version": "1.1.1", "Authors@R": "c(\nperson(given = \"Anders Hugo\",\nfamily = \"Frelin\",\nemail = \"ahfrelin@g.ucla.edu\",\nrole = c(\"aut\")),\nperson(given = \"Helen\",\nfamily = \"Zhu\",\nrole = c(\"aut\"),\nemail = \"helen.zhu@mail.utoronto.ca\"),\nperson(given = \"Paul C.\",\nfamily = \"Boutros\",\nrole = c(\"aut\", \"cre\"),\nemail = \"PBoutros@sbpdiscovery.org\",\ncomment = c(ORCID = \"0000-0003-0553-7520\"))\n)", "Description": "A method that analyzes quality control metrics from\nmulti-sample genomic sequencing studies and nominates poor\nquality samples for exclusion. Per sample quality control data\nare transformed into z-scores and aggregated. The distribution\nof aggregated z-scores are modelled using parametric\ndistributions. The parameters of the optimal model, selected\neither by goodness-of-fit statistics or user-designation, are\nused for outlier nomination. Two implementations of the Cosine\nSimilarity Outlier Detection algorithm are provided with\nflexible parameters for dataset customization.", "Config/testthat/edition": "3", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 07:21:35 UTC", "User": "root" }, "Author": "Anders Hugo Frelin [aut], Helen Zhu [aut], Paul C. Boutros\n[aut, cre] (ORCID: )", "Maintainer": "Paul C. Boutros ", "Config/pak/sysreqs": "libjpeg-dev libpng-dev", "Repository": "https://pboutros.r-universe.dev", "Date/Publication": "2026-01-24 02:26:29 UTC", "RemoteUrl": "https://github.com/cran/OmicsQC", "RemoteRef": "HEAD", "RemoteSha": "b26f8975fe26cfc80a760024ad94b2fbed93f03b", "MD5sum": "021515a5fda5b33ac89d85d25e15df16", "_user": "pboutros", "_type": "src", "_file": "OmicsQC_1.1.1.tar.gz", "_fileid": "0b133ed98c698e99c152e48251a1472dfd0dbed88b0202e54a011f7125dffca3", "_filesize": 2055268, "_sha256": "0b133ed98c698e99c152e48251a1472dfd0dbed88b0202e54a011f7125dffca3", "_created": "2026-05-28T07:21:35.000Z", "_published": "2026-05-28T07:26:26.068Z", "_distro": "noble", "_jobs": [ { "job": 78242926306, "time": 132, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7259995219" }, { "job": 78242926248, "time": 147, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7259999802" }, { "job": 78242926197, "time": 71, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7259997148" }, { "job": 78242926262, "time": 100, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7260035253" }, { "job": 78242523240, "time": 169, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7259955453" }, { "job": 78242926192, "time": 112, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7259988692" }, { "job": 78242926235, "time": 81, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7259979268" }, { "job": 78242926362, "time": 77, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7259978143" }, { "job": 78242926220, "time": 73, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7259977091" } ], "_buildurl": "https://github.com/r-universe/pboutros/actions/runs/26560579940", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/OmicsQC", "_commit": { "id": "b26f8975fe26cfc80a760024ad94b2fbed93f03b", "author": "Paul C. 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"Sum across sign corrected z-scores for total sample quality score", "topics": [ "accumulate.zscores" ] }, { "page": "correct.zscore.signs", "title": "Corrects the z-scores signs according to the metrics", "topics": [ "correct.zscore.signs" ] }, { "page": "cosine.similarity.cutoff", "title": "Calculate an outlier cutoff using cosine similarity", "topics": [ "cosine.similarity.cutoff" ] }, { "page": "cosine.similarity.iterative", "title": "Tests the accumulated quality scores for outliers using cosine similarity", "topics": [ "cosine.similarity.iterative" ] }, { "page": "example.qc.dataframe", "title": "QC metrics across 100 samples", "topics": [ "example.qc.dataframe" ] }, { "page": "fit.and.evaluate", "title": "Fits the QC data to distributions and returns the KS test result and BIC score", "topics": [ "fit.and.evaluate" ] }, { "page": "get.qc.barplot", "title": "Generates the standard barplot of scores for each sample", "topics": [ "get.qc.barplot" ] }, { "page": "get.qc.heatmap", "title": "Generates the standard heatmap of scores for each sample.", "topics": [ "get.qc.heatmap" ] }, { "page": "get.qc.multipanelplot", "title": "Generates the multipanel plot of heatmap and barplot", "topics": [ "get.qc.multipanelplot" ] }, { "page": "sign.correction", "title": "Directionality of QC metrics", "topics": [ "sign.correction" ] }, { "page": "ylabels", "title": "Formatted QC metrics labels", "topics": [ "ylabels" ] }, { "page": "zscores.from.metrics", "title": "Calculate z-scores for each metric across each sample", "topics": [ "zscores.from.metrics" ] } ], "_rundeps": [ "BoutrosLab.plotting.general", "class", "cli", "cluster", "deldir", "e1071", "fitdistrplus", "glue", "gridExtra", "gtable", "hexbin", "interp", "jpeg", "lattice", "latticeExtra", "lifecycle", "lsa", "MASS", "Matrix", "png", "proxy", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "SnowballC", "survival" ], "_vignettes": [ { "source": "Intro_to_omicsQC.Rmd", "filename": "Intro_to_omicsQC.html", "title": 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