recipe bioconductor-deqms

a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

Homepage:

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

License:

LGPL

Recipe:

/bioconductor-deqms/meta.yaml

DEqMS is developped on top of Limma. However, Limma assumes same prior variance for all genes. In proteomics, the accuracy of protein abundance estimates varies by the number of peptides/PSMs quantified in both label-free and labelled data. Proteins quantification by multiple peptides or PSMs are more accurate. DEqMS package is able to estimate different prior variances for proteins quantified by different number of PSMs/peptides, therefore acchieving better accuracy. The package can be applied to analyze both label-free and labelled proteomics data.

package bioconductor-deqms

(downloads) docker_bioconductor-deqms

Versions:
1.28.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.11.1-0,  1.10.0-0,  1.8.0-1,  1.8.0-0, 

1.28.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.11.1-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.1-1,  1.0.1-0,  1.0.0-1,  1.0.0-0

Depends:

  • on bioconductor-limma >=3.66.0,<3.67.0

  • on r-base >=4.5,<4.6.0a0

  • on r-dplyr

  • on r-ggplot2

  • on r-matrixstats

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-deqms

to add into an existing workspace instead, run:

pixi add bioconductor-deqms

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-deqms

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-deqms

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-deqms:<tag>

(see bioconductor-deqms/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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