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LOBSTAHS

This is the development version of LOBSTAHS; for the stable release version, see LOBSTAHS.

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences


Bioconductor version: Development (3.20)

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.

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 at whoi.edu>, Daniel Lowenstein <dlowenstein at whoi.edu>, James Collins <james.r.collins at aya.yale.edu>

Citation (from within R, enter citation("LOBSTAHS")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("LOBSTAHS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("LOBSTAHS")
Discovery, Identification, and Screening of Lipids and Oxylipins in HPLC-MS Datasets Using LOBSTAHS HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, ImmunoOncology, Lipidomics, MassSpectrometry, Metabolomics, Software
Version 1.31.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL (>= 3) + file LICENSE
Depends R (>= 3.4), xcms, CAMERA, methods
Imports utils
System Requirements
URL http://bioconductor.org/packages/LOBSTAHS
Bug Reports https://github.com/vanmooylipidomics/LOBSTAHS/issues/new
See More
Suggests PtH2O2lipids, knitr, rmarkdown
Linking To
Enhances
Depends On Me PtH2O2lipids
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package LOBSTAHS_1.31.0.tar.gz
Windows Binary LOBSTAHS_1.31.0.zip
macOS Binary (x86_64) LOBSTAHS_1.31.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/LOBSTAHS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/LOBSTAHS
Bioc Package Browser https://code.bioconductor.org/browse/LOBSTAHS/
Package Short Url https://bioconductor.org/packages/LOBSTAHS/
Package Downloads Report Download Stats