- recipe bioconductor-clustcomp
Clustering Comparison Package
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/clustComp.html
- License:
GPL (>= 2)
- Recipe:
- Links:
biotools: clustcomp, doi: 10.1038/nmeth.3252
clustComp is a package that implements several techniques for the comparison and visualisation of relationships between different clustering results, either flat versus flat or hierarchical versus flat. These relationships among clusters are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection; the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness. The best layout of the bi-graph is provided by the barycentre algorithm, which minimises the weighted number of crossings. In the case of comparing a hierarchical and a non-hierarchical clustering, the dendrogram is pruned at different heights, selected by exploring the tree by depth-first search, starting at the root. Branches are decided to be split according to the value of a scoring function, that can be based either on the aesthetics of the bi-graph or on the mutual information between the hierarchical and the flat clusterings. A mapping between groups of clusters from each side is constructed with a greedy algorithm, and can be additionally visualised.
- package bioconductor-clustcomp¶
- Versions:
1.38.0-0,1.34.0-0,1.30.0-1,1.30.0-0,1.28.0-0,1.26.0-0,1.22.0-0,1.20.0-0,1.18.0-1,1.38.0-0,1.34.0-0,1.30.0-1,1.30.0-0,1.28.0-0,1.26.0-0,1.22.0-0,1.20.0-0,1.18.0-1,1.18.0-0,1.16.0-0,1.14.0-0,1.12.0-1,1.12.0-0,1.10.0-0,1.8.0-0,1.6.0-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-sm
- 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-clustcomp
to add into an existing workspace instead, run:
pixi add bioconductor-clustcomp
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-clustcomp
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-clustcomp
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-clustcomp:<tag>
(see bioconductor-clustcomp/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-clustcomp/README.html)
