recipe bioconductor-cnvfilter

Identifies false positives of CNV calling tools by using SNV calls

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-cnvfilter/meta.yaml

CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.

package bioconductor-cnvfilter

versions:

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.1-0,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-copynumberplots:

>=1.18.0,<1.19.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-karyoploter:

>=1.28.0,<1.29.0

depends bioconductor-regioner:

>=1.34.0,<1.35.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-pracma:

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-cnvfilter

and update with::

   mamba update bioconductor-cnvfilter

To create a new environment, run:

mamba create --name myenvname bioconductor-cnvfilter

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-cnvfilter:<tag>

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

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