LOBSTAHS

DOI: 10.18129/B9.bioc.LOBSTAHS    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see LOBSTAHS.

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	DataImport, ImmunoOncology, Lipidomics, MassSpectrometry, Metabolomics, Software
Version	1.22.0
In Bioconductor since	BioC 3.4 (R-3.3) (6 years)
License	GPL (>= 3) + file LICENSE
Depends	R (>= 3.4), xcms, CAMERA, methods
Imports	utils
LinkingTo
Suggests	PtH2O2lipids, knitr, rmarkdown
SystemRequirements
Enhances
URL	http://bioconductor.org/packages/LOBSTAHS
BugReports	https://github.com/vanmooylipidomics/LOBSTAHS/issues/new
Depends On Me	PtH2O2lipids
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	LOBSTAHS_1.22.0.tar.gz
Windows Binary	LOBSTAHS_1.22.0.zip
macOS Binary (x86_64)	LOBSTAHS_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LOBSTAHS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LOBSTAHS
Package Short Url	https://bioconductor.org/packages/LOBSTAHS/
Package Downloads Report	Download Stats