- recipe bioconductor-mdp
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
- Homepage:
- License:
GPL-3
- Recipe:
The Molecular Degree of Perturbation webtool quantifies the heterogeneity of samples. It takes a data.frame of omic data that contains at least two classes (control and test) and assigns a score to all samples based on how perturbed they are compared to the controls. It is based on the Molecular Distance to Health (Pankla et al. 2009), and expands on this algorithm by adding the options to calculate the z-score using the modified z-score (using median absolute deviation), change the z-score zeroing threshold, and look at genes that are most perturbed in the test versus control classes.
- package bioconductor-mdp¶
- Versions:
1.30.0-0,1.26.0-0,1.22.0-0,1.20.0-0,1.18.0-0,1.14.0-0,1.12.0-0,1.10.0-1,1.10.0-0,1.30.0-0,1.26.0-0,1.22.0-0,1.20.0-0,1.18.0-0,1.14.0-0,1.12.0-0,1.10.0-1,1.10.0-0,1.8.0-0,1.6.0-0,1.4.0-1,1.4.0-0,1.2.0-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-ggplot2
on r-gridextra
- 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-mdp
to add into an existing workspace instead, run:
pixi add bioconductor-mdp
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-mdp
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-mdp
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-mdp:<tag>
(see bioconductor-mdp/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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-mdp/README.html)
