- recipe cnv_facets
Detect somatic copy number variants (CNV) in tumour-normal samples using next generation sequencing data
- Homepage:
- License:
MIT / MIT
- Recipe:
- package cnv_facets¶
- versions:
0.16.0-1,0.16.0-0,0.15.0-1,0.15.0-0,0.14.0-1,0.13.0-1,0.12.1-1,0.12.1-0,0.12.0-0,0.16.0-1,0.16.0-0,0.15.0-1,0.15.0-0,0.14.0-1,0.13.0-1,0.12.1-1,0.12.1-0,0.12.0-0,v0.11.3-2,v0.11.3-1,v0.11.2-1- depends bcftools:
>=1.9- depends bioconductor-rsamtools:
- depends htslib:
>=1.9,<1.10.0a0- depends libgcc-ng:
>=7.3.0- depends libgfortran-ng:
>=7,<8.0a0- depends libstdcxx-ng:
>=7.3.0- depends python:
>=3.8,<3.9.0a0- depends r-base:
>=3.6,<3.7.0a0- depends r-data.table:
- depends r-ggplot2:
- depends r-gridextra:
- depends r-jsonlite:
- depends samtools:
- depends snp-pileup:
- 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 cnv_facets and update with:: mamba update cnv_facets
To create a new environment, run:
mamba create --name myenvname cnv_facets
with
myenvnamebeing 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/cnv_facets:<tag> (see `cnv_facets/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/cnv_facets/README.html)
