- recipe r-mobster
Model-based subclonal deconvolution from bulk sequencing.
- Homepage:
- Documentation:
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
MOBSTER is a package that implements a statistical model for tumour subclonal deconvolution which combines Dirichlet mixtures with distributions predicted by theoretical population genetics. The model implemented is a parametric (finite) mixture with multiple Beta components, and one Pareto power law tail. Beta components capture mutations that rise up in frequency by positive selection, and the Pareto tail models alleles resulting from neutral, intra-clone, evolutionary dynamics.
- package r-mobster¶
- Versions:
0.1.1-0- Depends:
on r-base
>=4.4,<4.5.0a0on r-cli
on r-clisymbols
on r-cowplot
on r-crayon
on r-dndscv
on r-dplyr
on r-easypar
on r-ggplot2
on r-ggpubr
on r-ggrepel
on r-ggthemes
on r-magrittr
on r-pio
on r-sads
on r-tidyr
on r-tidyverse
on r-vcfr
- 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-mobster
to add into an existing workspace instead, run:
pixi add r-mobster
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-mobster
Alternatively, to install into a new environment, run:
conda create -n envname r-mobster
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-mobster:<tag>
(see r-mobster/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-mobster/README.html)
