- recipe r-dndscv
dN/dS methods to quantify selection in cancer and somatic evolution.
- Homepage:
- Documentation:
https://htmlpreview.github.io/?http://github.com/im3sanger/dndscv/blob/master/vignettes/dNdScv.html
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
Description: This package contains functions for studying selection on coding sequences using a Poisson implementation of dN/dS. A Poisson model of dN/dS facilitates the study of selection beyond traditional codon models, including complex context-dependent mutation effects and selection on nonsense and splice site mutations. This model is best suited for resequencing studies, with very low density of mutations per base pair. The model was initially developed for cancer genome sequencing studies, and specific functions are provided to perform driver gene discovery using the dNdScv method on human cancer genomic data.
- package r-dndscv¶
- Versions:
0.1.0-0- Depends:
on bioconductor-biostrings
on bioconductor-genomicranges
on bioconductor-iranges
on bioconductor-rsamtools
on r-base
>=4.4,<4.5.0a0on r-mass
on r-plyr
on r-poilog
on r-seqinr
- 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-dndscv
to add into an existing workspace instead, run:
pixi add r-dndscv
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-dndscv
Alternatively, to install into a new environment, run:
conda create -n envname r-dndscv
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-dndscv:<tag>
(see r-dndscv/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-dndscv/README.html)
