DESCRIPTION

Package: LOBSTAHS
Title: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Version: 1.23.0
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>