recipe bioconductor-specl

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Homepage:

https://bioconductor.org/packages/3.20/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:
1.44.0-0,  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, 

1.44.0-0,  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:

  • on r-base >=4.5,<4.6.0a0

  • on r-dbi >=0.5

  • on r-protviz >=0.7

  • on r-rsqlite >=1.1

  • on r-seqinr >=3.3

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-specl

to add into an existing workspace instead, run:

pixi add bioconductor-specl

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-specl

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-specl

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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