recipe bioconductor-msmstests

LC-MS/MS Differential Expression Tests

Homepage:

https://bioconductor.org/packages/3.18/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:
1.40.0-0,  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, 

1.40.0-0,  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 bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-msmseda:

>=1.40.0,<1.41.0

depends bioconductor-msnbase:

>=2.28.0,<2.29.0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0

depends r-base:

>=4.3,<4.4.0a0

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-msmstests

and update with::

   mamba update bioconductor-msmstests

To create a new environment, run:

mamba create --name myenvname bioconductor-msmstests

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-msmstests:<tag>

(see `bioconductor-msmstests/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-msmstests/README.html)