recipe bioconductor-pth2o2lipids

  1. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015)

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/PtH2O2lipids.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-pth2o2lipids/meta.yaml

Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots.

package bioconductor-pth2o2lipids

(downloads) docker_bioconductor-pth2o2lipids

versions:
1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0, 

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-1,  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,  1.8.0-0

depends bioconductor-camera:

>=1.58.0,<1.59.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-lobstahs:

>=1.28.0,<1.29.0

depends bioconductor-xcms:

>=4.0.0,<4.1.0

depends curl:

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-pth2o2lipids

and update with::

   mamba update bioconductor-pth2o2lipids

To create a new environment, run:

mamba create --name myenvname bioconductor-pth2o2lipids

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-pth2o2lipids:<tag>

(see `bioconductor-pth2o2lipids/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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