- recipe bioconductor-snm
Supervised Normalization of Microarrays
- Homepage:
- License:
LGPL
- Recipe:
- Links:
biotools: snm
SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.
- package bioconductor-snm¶
- Versions:
1.58.0-0,1.54.0-0,1.50.0-0,1.48.0-0,1.46.0-0,1.42.0-0,1.40.0-0,1.38.0-1,1.38.0-0,1.58.0-0,1.54.0-0,1.50.0-0,1.48.0-0,1.46.0-0,1.42.0-0,1.40.0-0,1.38.0-1,1.38.0-0,1.36.0-0,1.34.0-0,1.32.0-1,1.32.0-0,1.30.0-0,1.28.0-0,1.26.0-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-corpcor
on r-lme4
>=1.0
- 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-snm
to add into an existing workspace instead, run:
pixi add bioconductor-snm
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-snm
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-snm
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-snm:<tag>
(see bioconductor-snm/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-snm/README.html)
