recipe bioconductor-simat

GC-SIM-MS data processing and alaysis tool

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-simat/meta.yaml

Links:

biotools: simat, doi: 10.1186/s12859-015-0681-2

This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.

package bioconductor-simat

(downloads) docker_bioconductor-simat

versions:
1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.26.0-2,  1.26.0-1,  1.26.0-0,  1.24.0-0, 

1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.26.0-2,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.14.0-0,  1.10.0-0

depends bioconductor-mzr:

>=2.40.0,<2.41.0

depends bioconductor-mzr:

>=2.40.0,<2.41.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

depends r-rcpp:

>=0.11.3

depends r-reshape2:

requirements:

additional platforms:

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-simat

and update with::

   mamba update bioconductor-simat

To create a new environment, run:

mamba create --name myenvname bioconductor-simat

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-simat:<tag>

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

Download stats

Link to this page

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

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-simat/README.html)