recipe r-tinc

TINC is a package that implements algorithms to determine the contamination of a bulk sequencing sample in the context of cancer studies (matched tumour/ normal). The contamination estimated by TINC can be either due to normal cells sampled in the tumour biopsy or to tumour cells in the normal biopsy. The former case is traditionally called purity, or cellularity, and a number of tools exist to estimate it. The latter case is less common, and that is the main reason TINC has been developed. For this reason, the package takes name TINC, Tumour-in-Normal contamination. TINC is part of the evoverse, a package that gathers multiple R packages to implement Cancer Evolution analyses.

Homepage:

https://github.com/caravagnalab/TINC

License:

GPL3 / GPL-3

Recipe:

/r-tinc/meta.yaml

package r-tinc

versions:

0.1.0-0

depends r-base:

>=4.4,<4.5.0a0

depends r-bmix:

depends r-cli:

depends r-cnaqc:

depends r-cowplot:

depends r-crayon:

depends r-dplyr:

depends r-ggplot2:

depends r-ggpubr:

depends r-ggrepel:

depends r-mobster:

depends r-pio:

depends r-purrr:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-vcfr:

depends r-viber:

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-tinc

and update with::

   mamba update r-tinc

To create a new environment, run:

mamba create --name myenvname r-tinc

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-tinc:<tag>

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

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