- recipe bioconductor-varcon
VarCon: an R package for retrieving neighboring nucleotides of an SNV
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¶
- depends bioconductor-biostrings:
- depends bioconductor-bsgenome:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends r-base:
- depends r-ggplot2:
- depends r-shiny:
- depends r-shinycssloaders:
- depends r-shinyfiles:
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
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/bioconductor-varcon:<tag> (see `bioconductor-varcon/tags`_ for valid values for ``<tag>``)