- 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:
- License:
GPL3 / GPL-3
- Recipe:
- package r-tinc¶
- Versions:
0.1.0-0- Depends:
on r-base
>=4.4,<4.5.0a0on r-bmix
on r-cli
on r-cnaqc
on r-cowplot
on r-crayon
on r-dplyr
on r-ggplot2
on r-ggpubr
on r-ggrepel
on r-mobster
on r-pio
on r-purrr
on r-stringr
on r-tibble
on r-tidyr
on r-vcfr
on r-viber
- 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-tinc
to add into an existing workspace instead, run:
pixi add r-tinc
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-tinc
Alternatively, to install into a new environment, run:
conda create -n envname r-tinc
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-tinc:<tag>
(see r-tinc/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-tinc/README.html)
