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

## Documentation for package ‘VarCon’ version 1.19.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

calculateHZEIperNT | Generates table with HZEI scores per nucleotide of a sequence.
calculateMaxEntScanScore | Calculate MaxEntScan score of a splice site sequence
gene2transcript | Small data frame specifying a transcript to certain genes for synonymous use.
generateHEXplorerPlot | Generates plot with HZEI values and splice site strengths from a list holding information about an SNV.
getMaxEntInfo | Generates table with MaxEntScan scores per potential SA position.
getSeqInfoFromVariation | Collects information about genomic context of sequence variants.
hbg | Donor sequences and their HBS
hex | Hexamers and Z scores
prepareReferenceFasta | Imports Fasta file from filepath.
referenceDnaStringSet | Small DNAStringset as exemplary reference genome sequence
startVarConApp | Start GUI of VarCon.
transCoord | Small table as exemplary transcript table with exon coordinates