recipe r-ctree

Clone trees for Cancer Evolution studies from bulk sequencing data.

Homepage:

https://github.com/caravagnalab/ctree

Documentation:

https://caravagnalab.github.io/ctree/

License:

GPL3 / GPL-3.0-or-later

Recipe:

/r-ctree/meta.yaml

The ctree package implements clones trees for cancer evolutionary studies. These models are built from Cancer Cell Franctions (CCFs) clusters computed via tumour subclonal deconvolution, using either one or more tumour biopsies at once. They can be used to model evolutionary trajectories from bulk sequencing data, especially if whole-genome sequencing is available. The package implements S3 objects for the mutation trees, as well as a Monte Carlo sampler to generate them, as well as functions to plot and analyze the trees. The sibling of a clone tree is a mutation tree, which is built from binary mutation profiles; refer to the mtree package for mutation trees.

package r-ctree

versions:

1.1.0-0

depends r-base:

>=4.4,<4.5.0a0

depends r-cli:

depends r-clisymbols:

depends r-covr:

depends r-crayon:

depends r-dplyr:

depends r-easypar:

depends r-entropy:

depends r-ggplot2:

depends r-ggraph:

depends r-ggrepel:

depends r-igraph:

depends r-knitr:

depends r-matrixcalc:

depends r-matrixstats:

depends r-pio:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rmarkdown:

depends r-tidygraph:

depends r-tidyverse:

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 r-ctree

and update with::

   mamba update r-ctree

To create a new environment, run:

mamba create --name myenvname r-ctree

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/r-ctree:<tag>

(see `r-ctree/tags`_ for valid values for ``<tag>``)

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/r-ctree/README.html)