Package Recipe 'bioconductor-oncosimulr'

recipe bioconductor-oncosimulr

Forward Genetic Simulation of Cancer Progression with Epistasis

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/OncoSimulR.html
License:: GPL (>= 3)
Recipe:: /bioconductor-oncosimulr/meta.yaml
Links:: biotools: oncosimulr

Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Fitness (including just birth, just death, or both birth and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, additive, NK, Ising, and Eggbox models) and plotting them.

package bioconductor-oncosimulr¶

Versions:

4.12.0-0, 4.8.0-0, 4.4.0-0, 4.2.0-0, 4.0.0-0, 3.2.0-2, 3.2.0-1, 3.2.0-0, 3.0.0-0,

4.12.0-0, 4.8.0-0, 4.4.0-0, 4.2.0-0, 4.0.0-0, 3.2.0-2, 3.2.0-1, 3.2.0-0, 3.0.0-0, 2.20.0-1, 2.20.0-0, 2.18.0-0, 2.16.0-0, 2.14.0-1, 2.12.0-0, 2.10.0-0, 2.8.0-0

Depends:

on bioconductor-graph >=1.88.0,<1.89.0
on bioconductor-graph >=1.88.1,<1.89.0a0
on bioconductor-rgraphviz >=2.54.0,<2.55.0
on bioconductor-rgraphviz >=2.54.0,<2.55.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-car
on r-data.table
on r-dplyr
on r-ggplot2
on r-ggrepel
on r-gtools
on r-igraph
on r-rcolorbrewer
on r-rcpp >=0.12.4
on r-smatr
on r-stringr

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-oncosimulr

to add into an existing workspace instead, run:

pixi add bioconductor-oncosimulr

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-oncosimulr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-oncosimulr

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-oncosimulr:<tag>

(see bioconductor-oncosimulr/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-oncosimulr/README.html)