recipe bioconductor-specl

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-specl/meta.yaml

Links:

biotools: specl

provides a functions for generating spectra libraries that can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>.

package bioconductor-specl

(downloads) docker_bioconductor-specl

versions:
1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0, 

1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.1-0,  1.14.0-0,  1.12.0-0

depends r-base:

>=4.4,<4.5.0a0

depends r-dbi:

>=0.5

depends r-protviz:

>=0.7

depends r-rsqlite:

>=1.1

depends r-seqinr:

>=3.3

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-specl

and update with::

   mamba update bioconductor-specl

To create a new environment, run:

mamba create --name myenvname bioconductor-specl

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-specl:<tag>

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

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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-specl/README.html)