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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
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Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Bioconductor version: Release (3.5)
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 |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | DataImport, Lipidomics, MassSpectrometry, Metabolomics, Software |
| Version | 1.2.1 |
| In Bioconductor since | BioC 3.4 (R-3.3) (1 year) |
| 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.
| Source Package | LOBSTAHS_1.2.1.tar.gz |
| Windows Binary | LOBSTAHS_1.2.1.zip |
| Mac OS X 10.11 (El Capitan) | LOBSTAHS_1.2.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/LOBSTAHS |
| Package Short Url | http://bioconductor.org/packages/LOBSTAHS/ |
| Package Downloads Report | Download Stats |
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