- recipe bioconductor-verso
Viral Evolution ReconStructiOn (VERSO)
- Homepage:
- License:
file LICENSE
- Recipe:
Mutations that rapidly accumulate in viral genomes during a pandemic can be used to track the evolution of the virus and, accordingly, unravel the viral infection network. To this extent, sequencing samples of the virus can be employed to estimate models from genomic epidemiology and may serve, for instance, to estimate the proportion of undetected infected people by uncovering cryptic transmissions, as well as to predict likely trends in the number of infected, hospitalized, dead and recovered people. VERSO is an algorithmic framework that processes variants profiles from viral samples to produce phylogenetic models of viral evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a log-likelihood function. VERSO includes two separate and subsequent steps; in this package we provide an R implementation of VERSO STEP 1.
- package bioconductor-verso¶
- Versions:
1.20.0-0,1.16.0-0,1.12.0-1,1.12.0-0,1.10.0-0,1.8.0-0,1.4.0-0,1.2.0-0,1.0.0-1,1.20.0-0,1.16.0-0,1.12.0-1,1.12.0-0,1.10.0-0,1.8.0-0,1.4.0-0,1.2.0-0,1.0.0-1,1.0.0-0- Depends:
on r-ape
on r-base
>=4.5,<4.6.0a0on r-data.tree
on r-rfast
- 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-verso
to add into an existing workspace instead, run:
pixi add bioconductor-verso
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-verso
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-verso
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-verso:<tag>
(see bioconductor-verso/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-verso/README.html)
