recipe bioconductor-varcon

VarCon: an R package for retrieving neighboring nucleotides of an SNV

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/VarCon.html

License:

GPL-3

Recipe:

/bioconductor-varcon/meta.yaml

VarCon is an R package which converts the positional information from the annotation of an single nucleotide variation (SNV) (either referring to the coding sequence or the reference genomic sequence). It retrieves the genomic reference sequence around the position of the single nucleotide variation. To asses, whether the SNV could potentially influence binding of splicing regulatory proteins VarCon calcualtes the HEXplorer score as an estimation. Besides, VarCon additionally reports splice site strengths of splice sites within the retrieved genomic sequence and any changes due to the SNV.

package bioconductor-varcon

versions:

1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-bsgenome:

>=1.74.0,<1.75.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

depends r-shiny:

depends r-shinycssloaders:

depends r-shinyfiles:

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 bioconductor-varcon

and update with::

   mamba update bioconductor-varcon

To create a new environment, run:

mamba create --name myenvname bioconductor-varcon

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-varcon:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

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