- recipe r-mixkernel
Kernel-based methods are powerful methods for integrating heterogeneous types of data. mixKernel aims at providing methods to combine kernel for unsupervised exploratory analysis. Different solutions are provided to compute a meta-kernel, in a consensus way or in a way that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a non linear space and from the multiple source point of view. Functions to assess and display important variables are also provided in the package. Jerome Mariette and Nathalie Villa-Vialaneix (2017) <doi:10.1093/bioinformatics/btx682>.
- Homepage:
- License:
GPL3 / GPL (>= 2)
- Recipe:
- package r-mixkernel¶
- Versions:
0.9-1,0.9-0,0.8-2,0.8-1,0.8-0,0.7-0,0.6-0,0.5-2,0.5-1,0.9-1,0.9-0,0.8-2,0.8-1,0.8-0,0.7-0,0.6-0,0.5-2,0.5-1,0.5-0,0.4-2,0.4-1,0.4-0,0.3-1,0.3-0- Depends:
on bioconductor-mixomics
on bioconductor-phyloseq
on r-base
>=4.5,<4.6.0a0on r-corrplot
on r-ggplot2
on r-ldrtools
on r-markdown
on r-matrix
on r-psych
on r-quadprog
on r-reticulate
>=1.14on r-vegan
- 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 r-mixkernel
to add into an existing workspace instead, run:
pixi add r-mixkernel
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 r-mixkernel
Alternatively, to install into a new environment, run:
conda create -n envname r-mixkernel
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/r-mixkernel:<tag>
(see r-mixkernel/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/r-mixkernel/README.html)
