- recipe r-ctree
Clone trees for Cancer Evolution studies from bulk sequencing data.
- Homepage:
- Documentation:
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
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:
on r-base
>=4.4,<4.5.0a0on r-cli
on r-clisymbols
on r-covr
on r-crayon
on r-dplyr
on r-easypar
on r-entropy
on r-ggplot2
on r-ggraph
on r-ggrepel
on r-igraph
on r-knitr
on r-matrixcalc
on r-matrixstats
on r-pio
on r-rcolorbrewer
on r-reshape2
on r-rmarkdown
on r-tidygraph
on r-tidyverse
- 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-ctree
to add into an existing workspace instead, run:
pixi add r-ctree
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-ctree
Alternatively, to install into a new environment, run:
conda create -n envname r-ctree
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-ctree:<tag>
(see r-ctree/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-ctree/README.html)
