recipe bioconductor-msqrob2

Robust statistical inference for quantitative LC-MS proteomics

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/msqrob2.html

License:

Artistic-2.0

Recipe:

/bioconductor-msqrob2/meta.yaml

msqrob2 provides a robust linear mixed model framework for assessing differential abundance in MS-based Quantitative proteomics experiments. Our workflows can start from raw peptide intensities or summarised protein expression values. The model parameter estimates can be stabilized by ridge regression, empirical Bayes variance estimation and robust M-estimation. msqrob2's hurde workflow can handle missing data without having to rely on hard-to-verify imputation assumptions, and, outcompetes state-of-the-art methods with and without imputation for both high and low missingness. It builds on QFeature infrastructure for quantitative mass spectrometry data to store the model results together with the raw data and preprocessed data.

package bioconductor-msqrob2

versions:

1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-multiassayexperiment:

>=1.32.0,<1.33.0

depends bioconductor-qfeatures:

>=1.16.0,<1.17.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-codetools:

depends r-lme4:

depends r-mass:

depends r-matrix:

depends r-purrr:

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-msqrob2

and update with::

   mamba update bioconductor-msqrob2

To create a new environment, run:

mamba create --name myenvname bioconductor-msqrob2

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-msqrob2:<tag>

(see `bioconductor-msqrob2/tags`_ for valid values for ``<tag>``)

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