recipe bioconductor-varcon

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

Homepage:

https://bioconductor.org/packages/3.16/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:

1.6.0-0,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• r-base >=4.2,<4.3.0a0

• r-ggplot2

• r-shiny

• r-shinycssloaders

• r-shinyfiles

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-varcon

and update with:

conda update bioconductor-varcon

or 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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