recipe bioconductor-tronco

TRONCO, an R package for TRanslational ONCOlogy

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/TRONCO.html

License:

GPL-3

Recipe:

/bioconductor-tronco/meta.yaml

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:

2.34.0-0,  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, 

2.34.0-0,  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 bioconductor-rgraphviz:

>=2.46.0,<2.47.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bnlearn:

depends r-circlize:

depends r-doparallel:

depends r-foreach:

depends r-gridextra:

depends r-gtable:

depends r-gtools:

depends r-igraph:

depends r-iterators:

depends r-r.matlab:

depends r-rcolorbrewer:

depends r-scales:

depends r-xtable:

requirements:

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-tronco

and update with::

   mamba update bioconductor-tronco

To create a new environment, run:

mamba create --name myenvname bioconductor-tronco

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-tronco:<tag>

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

Download stats

Link to this page

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