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() overdispFromBoots(): Parse the output from salmon