recipe bioconductor-msqrob2

Robust statistical inference for quantitative LC-MS proteomics

Homepage:

https://bioconductor.org/packages/3.16/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:

1.6.0-0,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-multiassayexperiment >=1.24.0,<1.25.0

• bioconductor-qfeatures >=1.8.0,<1.9.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-codetools

• r-lme4

• r-mass

• r-matrix

• r-purrr

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-msqrob2

and update with:

conda update bioconductor-msqrob2

or 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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