recipe bioconductor-oncosimulr

Forward Genetic Simulation of Cancer Progression with Epistasis

Homepage:

https://bioconductor.org/packages/3.18/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:

4.8.0-0,  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, 

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 bioconductor-graph:

>=1.84.0,<1.85.0

depends bioconductor-graph:

>=1.84.0,<1.85.0a0

depends bioconductor-rgraphviz:

>=2.50.0,<2.51.0

depends bioconductor-rgraphviz:

>=2.50.0,<2.51.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-car:

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-ggrepel:

depends r-gtools:

depends r-igraph:

depends r-rcolorbrewer:

depends r-rcpp:

>=0.12.4

depends r-smatr:

depends r-stringr:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-oncosimulr

and update with::

   mamba update bioconductor-oncosimulr

To create a new environment, run:

mamba create --name myenvname bioconductor-oncosimulr

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-oncosimulr:<tag>

(see `bioconductor-oncosimulr/tags`_ for valid values for ``<tag>``)

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