Package index • transmogR

Modify a Reference

indelcator(): Substitute InDels into one or more sequences

owl(): OverWrite Letters in an XStringSet

genomogrify(): Mogrify a genome using a set of variants

transmogrify(): Mogrify a transcriptome using a set of variants

Additional Functions

parY(): Get the PAR-Y Regions From a Seqinfo Object

cleanVariants(): Check provided variants for compatibility

overlapsByVar(): Count overlaps by variant type

shiftByVar(): Calculate new exon co-ordinates

upsetVarByCol(): Show Variants by Impacted Columns

varTags(): Create a set of tags indicating overlap status with variants

varTypes(): Identify SNVs, Insertions and Deletions

sjFromExons(): Obtain Splice-Junctions from Exons and Transcripts

digestSalmon(): Parse the output from salmon