- recipe bioconductor-tronco
TRONCO, an R package for TRanslational ONCOlogy
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/TRONCO.html
- License:
GPL-3
- Recipe:
The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference (PICNIC).
- package bioconductor-tronco¶
- Versions:
2.42.0-0,2.38.0-0,2.34.0-0,2.32.0-0,2.30.0-0,2.26.0-0,2.24.0-0,2.22.0-1,2.22.0-0,2.42.0-0,2.38.0-0,2.34.0-0,2.32.0-0,2.30.0-0,2.26.0-0,2.24.0-0,2.22.0-1,2.22.0-0,2.20.0-0,2.18.0-0,2.16.2-0,2.14.2-0- Depends:
on bioconductor-rgraphviz
>=2.54.0,<2.55.0on r-base
>=4.5,<4.6.0a0on r-bnlearn
on r-circlize
on r-doparallel
on r-foreach
on r-gridextra
on r-gtable
on r-gtools
on r-igraph
on r-iterators
on r-r.matlab
on r-rcolorbrewer
on r-scales
on r-xtable
- 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-tronco
to add into an existing workspace instead, run:
pixi add bioconductor-tronco
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-tronco
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-tronco
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-tronco:<tag>
(see bioconductor-tronco/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/bioconductor-tronco/README.html)
