- recipe bioconductor-rlassocox
A reweighted Lasso-Cox by integrating gene interaction information
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/RLassoCox.html
- License:
Artistic-2.0
- Recipe:
RLassoCox is a package that implements the RLasso-Cox model proposed by Wei Liu. The RLasso-Cox model integrates gene interaction information into the Lasso-Cox model for accurate survival prediction and survival biomarker discovery. It is based on the hypothesis that topologically important genes in the gene interaction network tend to have stable expression changes. The RLasso-Cox model uses random walk to evaluate the topological weight of genes, and then highlights topologically important genes to improve the generalization ability of the Lasso-Cox model. The RLasso-Cox model has the advantage of identifying small gene sets with high prognostic performance on independent datasets, which may play an important role in identifying robust survival biomarkers for various cancer types.
- package bioconductor-rlassocox¶
- Versions:
1.18.0-0,1.14.0-0,1.10.0-0,1.8.0-0,1.6.0-0,1.2.0-0,1.0.0-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-glmnet
on r-igraph
on r-matrix
on r-survival
- 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-rlassocox
to add into an existing workspace instead, run:
pixi add bioconductor-rlassocox
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-rlassocox
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-rlassocox
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-rlassocox:<tag>
(see bioconductor-rlassocox/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-rlassocox/README.html)
