LOBSTAHS
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see LOBSTAHS.
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Bioconductor version: 3.13
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: James Collins <james.r.collins at aya.yale.edu>, Henry Holm <hholm at whoi.edu>, Daniel Lowenstein <dlowenstein at whoi.edu>
citation("LOBSTAHS")):
Installation
To install this package, start R (version "4.1") 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")| Discovery, Identification, and Screening of Lipids and Oxylipins in HPLC-MS Datasets Using LOBSTAHS | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, ImmunoOncology, Lipidomics, MassSpectrometry, Metabolomics, Software |
| Version | 1.18.1 |
| 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_1.18.1.tar.gz |
| Windows Binary | LOBSTAHS_1.18.1.zip |
| macOS 10.13 (High Sierra) | LOBSTAHS_1.18.1.tgz |
| 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 |
| Old Source Packages for BioC 3.13 | Source Archive |