recipe bioconductor-lobstahs

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/LOBSTAHS.html

License:

GPL (>= 3) + file LICENSE

Recipe:

/bioconductor-lobstahs/meta.yaml

Links:

biotools: lobstahs

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.

package bioconductor-lobstahs

versions:

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0, 

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.1-0,  1.4.0-0

depends bioconductor-camera:

>=1.58.0,<1.59.0

depends bioconductor-xcms:

>=4.0.0,<4.1.0

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-lobstahs

and update with::

   mamba update bioconductor-lobstahs

To create a new environment, run:

mamba create --name myenvname bioconductor-lobstahs

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-lobstahs:<tag>

(see `bioconductor-lobstahs/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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