To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("LOBSTAHS")

In most cases, you don't need to download the package archive at all.

LOBSTAHS

 

   

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

Bioconductor version: Release (3.4)

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], Benjamin Van Mooy [aut]

Maintainer: James Collins <james.r.collins at aya.yale.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("LOBSTAHS")

Documentation

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, Lipidomics, MassSpectrometry, Metabolomics, Software
Version 1.0.0
In Bioconductor since BioC 3.4 (R-3.3) (< 6 months)
License GPL (>= 3) + file LICENSE
Depends R (>= 3.3), 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
Build Report  

Package Archives

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

Package Source LOBSTAHS_1.0.0.tar.gz
Windows Binary LOBSTAHS_1.0.0.zip
Mac OS X 10.9 (Mavericks) LOBSTAHS_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/LOBSTAHS/tree/release-3.4
Package Short Url http://bioconductor.org/packages/LOBSTAHS/
Package Downloads Report Download Stats

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