recipe bioconductor-msmstests

LC-MS/MS Differential Expression Tests

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/msmsTests.html

License:

GPL-2

Recipe:

/bioconductor-msmstests/meta.yaml

Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.

package bioconductor-msmstests

(downloads) docker_bioconductor-msmstests

Versions:
1.48.0-0,  1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0, 

1.48.0-0,  1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.20.1-0

Depends:

  • on bioconductor-edger >=4.8.0,<4.9.0

  • on bioconductor-msmseda >=1.48.0,<1.49.0

  • on bioconductor-msnbase >=2.36.0,<2.37.0

  • on bioconductor-qvalue >=2.42.0,<2.43.0

  • on r-base >=4.5,<4.6.0a0

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-msmstests

to add into an existing workspace instead, run:

pixi add bioconductor-msmstests

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-msmstests

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-msmstests

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-msmstests:<tag>

(see bioconductor-msmstests/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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