{ "_id": "6a1fda83b401979e73437650", "Package": "MatrixQCvis", "Type": "Package", "Title": "Shiny-based interactive data-quality exploration for omics data", "Version": "1.21.0", "Date": "2025-06-26", "Authors@R": "c(person(\"Thomas\", \"Naake\", role = c(\"aut\", \"cre\"), \nemail = \"thomasnaake@googlemail.com\",\ncomment = c(ORCID = \"0000-0001-7917-5580\")),\nperson(\"Wolfgang\", \"Huber\", role = c(\"aut\"),\nemail = \"wolfgang.huber@embl.de\",\ncomment = c(ORCID = \"0000-0002-0474-2218\")))", "VignetteBuilder": "knitr", "Description": "Data quality assessment is an integral part of preparatory\ndata analysis to ensure sound biological information retrieval.\nWe present here the MatrixQCvis package, which provides\nshiny-based interactive visualization of data quality metrics\nat the per-sample and per-feature level. It is broadly\napplicable to quantitative omics data types that come in\nmatrix-like format (features x samples). It enables the\ndetection of low-quality samples, drifts, outliers and batch\neffects in data sets. Visualizations include amongst others\nbar- and violin plots of the (count/intensity) values, mean vs\nstandard deviation plots, MA plots, empirical cumulative\ndistribution function (ECDF) plots, visualizations of the\ndistances between samples, and multiple types of dimension\nreduction plots. Furthermore, MatrixQCvis allows for\ndifferential expression analysis based on the limma (moderated\nt-tests) and proDA (Wald tests) packages. MatrixQCvis builds\nupon the popular Bioconductor SummarizedExperiment S4 class and\nenables thus the facile integration into existing workflows.\nThe package is especially tailored towards metabolomics and\nproteomics mass spectrometry data, but also allows to assess\nthe data quality of other data types that can be represented in\na SummarizedExperiment object.", "biocViews": "Visualization, ShinyApps, GUI, QualityControl,\nDimensionReduction, Metabolomics, Proteomics, Transcriptomics", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev perl python3 zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:06 UTC", "RemoteUrl": "https://github.com/bioc/MatrixQCvis", "RemoteRef": "HEAD", "RemoteSha": "03254d0f9055af56fd8eb546723c4f1d6b785ef5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 07:31:36 UTC", "User": "root" }, "Author": 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