Package: LOBSTAHS
Title: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy
        Sequences
Version: 1.36.0
Date: 2021-08-30
Authors@R: c(
    person("James", "Collins", email = "james.r.collins@aya.yale.edu", 
           role = c("aut", "cre")),
    person("Helen", "Fredricks", email = "hfredricks@whoi.edu", 
           role = c("aut")),
    person("Bethanie", "Edwards", email = "bedwards@whoi.edu", role = c("aut")),
    person("Benjamin", "Van Mooy", email = "bvanmooy@whoi.edu", 
           role = c("aut")),
    person("Daniel", "Lowenstein", email = "dlowenstein@whoi.edu", 
           role = c("aut")),
    person("Henry", "Holm", email = "hholm@whoi.edu", role = c("aut"))
    )
Depends: R (>= 3.4), xcms, CAMERA, methods
Imports: utils
Suggests: PtH2O2lipids, knitr, rmarkdown
Description: LOBSTAHS is a multifunction package for screening,
        annotation, and putative identification of mass spectral
        features in large, HPLC-MS lipid datasets. In silico data for a
        wide range of lipids, oxidized lipids, and oxylipins can be
        generated from user-supplied structural criteria with a
        database generation function. LOBSTAHS then applies these
        databases to assign putative compound identities to features in
        any high-mass accuracy dataset that has been processed using
        xcms and CAMERA. Users can then apply a series of orthogonal
        screening criteria based on adduct ion formation patterns,
        chromatographic retention time, and other properties, to
        evaluate and assign confidence scores to this list of
        preliminary assignments. During the screening routine, LOBSTAHS
        rejects assignments that do not meet the specified criteria,
        identifies potential isomers and isobars, and assigns a variety
        of annotation codes to assist the user in evaluating the
        accuracy 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,
        DataImport
NeedsCompilation: no
Author: James Collins [aut, cre], Helen Fredricks [aut], Bethanie
        Edwards [aut], Henry Holm [aut], Benjamin Van Mooy [aut],
        Daniel Lowenstein [aut]
Maintainer: Henry Holm <hholm@whoi.edu>, Daniel Lowenstein
 <dlowenstein@whoi.edu>, James Collins
 <james.r.collins@aya.yale.edu>
Config/pak/sysreqs: libglpk-dev make libicu-dev libxml2-dev
        libnetcdf-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:33:12 UTC
RemoteUrl: https://github.com/bioc/LOBSTAHS
RemoteRef: RELEASE_3_22
RemoteSha: b35ad6cefd6d3d3e6954bb9055194268bb7ca88b
Packaged: 2026-03-02 08:45:38 UTC; root
Built: R 4.5.2; ; 2026-03-02 08:48:40 UTC; windows
