{ "_id": "6a1aefdf1d7bb097a09f65d9", "Package": "LOBSTAHS", "Title": "Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy\nSequences", "Version": "1.39.0", "Date": "2021-08-30", "Authors@R": "c(\nperson(\"James\", \"Collins\", email = \"james.r.collins@aya.yale.edu\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Helen\", \"Fredricks\", email = \"hfredricks@whoi.edu\",\nrole = c(\"aut\")),\nperson(\"Bethanie\", \"Edwards\", email = \"bedwards@whoi.edu\", role = c(\"aut\")),\nperson(\"Benjamin\", \"Van Mooy\", email = \"bvanmooy@whoi.edu\",\nrole = c(\"aut\")),\nperson(\"Daniel\", \"Lowenstein\", email = \"dlowenstein@whoi.edu\",\nrole = c(\"aut\")),\nperson(\"Henry\", \"Holm\", email = \"hholm@whoi.edu\", role = c(\"aut\"))\n)", "Description": "LOBSTAHS is a multifunction package for screening,\nannotation, and putative identification of mass spectral\nfeatures in large, HPLC-MS lipid datasets. In silico data for a\nwide range of lipids, oxidized lipids, and oxylipins can be\ngenerated from user-supplied structural criteria with a\ndatabase generation function. LOBSTAHS then applies these\ndatabases to assign putative compound identities to features in\nany high-mass accuracy dataset that has been processed using\nxcms and CAMERA. Users can then apply a series of orthogonal\nscreening criteria based on adduct ion formation patterns,\nchromatographic retention time, and other properties, to\nevaluate and assign confidence scores to this list of\npreliminary assignments. During the screening routine, LOBSTAHS\nrejects assignments that do not meet the specified criteria,\nidentifies potential isomers and isobars, and assigns a variety\nof annotation codes to assist the user in evaluating the\naccuracy of each assignment.", "License": "GPL (>= 3) + file LICENSE", "URL": "http://bioconductor.org/packages/LOBSTAHS", "BugReports": "https://github.com/vanmooylipidomics/LOBSTAHS/issues/new", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, MassSpectrometry, Metabolomics, Lipidomics,\nDataImport", "NeedsCompilation": "no", "Author": "James Collins [aut, cre], Helen Fredricks [aut], Bethanie\nEdwards [aut], Henry Holm [aut], Benjamin Van Mooy [aut],\nDaniel Lowenstein [aut]", "Maintainer": "Henry Holm , Daniel Lowenstein\n, James Collins\n", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:43:50 UTC", 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HPLC-MS Datasets Using LOBSTAHS", "author": "James Collins", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Purpose", "Installing the LOBSTAHS package", "Install current production version", "Install \"no warranties\" development version with latest features", "Install dependencies:", "Install RTools:", "Install packages needed for installation from Github:", "Install LOBSTAHS:", "Install 'PtH2O2lipids,' containing example data & precursor xsAnnotate object:", "\"Operating instructions,\" part 1: Pre-processing", "Acquisition of HPLC-MS data suitable for LOBSTAHS", "File conversion", "Initial file conversion; saves converted file to a directory \"mzXML_ms1_two_mode\":", "Extract positive, negative mode scans, then save in separate directories:", "Pre-processing with xcms", "Final pre-processing with CAMERA", "\"Operating instructions,\" part 2: The LOBSTAHS databases", "A note about molecular diversity in the current databases", "Accessing the default databases", "Concept of operation: Using input tables", "Introduction to the four input tables", "The componentCompTable", "The acylRanges and oxyRanges tables", "The adductHierarchies table", "Modification of table data to create new database entries", "First scenario: Defining single compounds", "Second scenario: Defining entire lipid classes for which an iterative simulation is to be performed", "Saving of files", "Database generation using generateLOBdbase", "\"Operating instructions,\" part 3: Compound/biomarker identification and screening using doLOBscreen (or, the \"meat\" of LOBSTAHS)", "Follow-on analysis of screened data", "Package updates and improvements", "Copyright", "References", "Notes" ], "created": "2016-07-05 21:50:25", "modified": "2021-08-30 19:10:14", "commits": 70 } ], "_score": 6.962842681201242, "_indexed": true, "_nocasepkg": "lobstahs", "_universes": [ "bioc", "hholm", "vanmooylipidomics" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.39.0", "date": 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