recipe bioconductor-synapter

Label-free data analysis pipeline for optimal identification and quantitation

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-synapter/meta.yaml

The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.

package bioconductor-synapter

versions:

2.26.0-0,  2.24.0-0,  2.22.0-0,  2.14.0-1,  2.14.0-0,  2.12.0-0,  2.10.0-0,  2.8.0-1,  2.6.1-0, 

2.26.0-0,  2.24.0-0,  2.22.0-0,  2.14.0-1,  2.14.0-0,  2.12.0-0,  2.10.0-0,  2.8.0-1,  2.6.1-0,  2.2.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-cleaver:

>=1.40.0,<1.41.0

depends bioconductor-msnbase:

>=2.28.0,<2.29.0

depends bioconductor-multtest:

>=2.58.0,<2.59.0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0

depends r-base:

>=4.3,<4.4.0a0

depends r-lattice:

depends r-rcolorbrewer:

depends r-readr:

>=0.2

depends r-rmarkdown:

>=1.0

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-synapter

and update with::

   mamba update bioconductor-synapter

To create a new environment, run:

mamba create --name myenvname bioconductor-synapter

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-synapter:<tag>

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

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Link to this page

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