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

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Documentation for package ‘VarCon’ version 1.8.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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