Modify a set of reference sequences using a set of variants

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Documentation for package ‘transmogR’ version 1.3.6

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

Help Pages

digestSalmon	Parse the output from salmon
genomogrify	Mogrify a genome using a set of variants
genomogrify-method	Mogrify a genome using a set of variants
genomogrify-methods	Mogrify a genome using a set of variants
indelcator	Substitute InDels into one or more sequences
indelcator-method	Substitute InDels into one or more sequences
overlapsByVar	Count overlaps by variant type
overlapsByVar-method	Count overlaps by variant type
overlapsByVar-methods	Count overlaps by variant type
owl	OverWrite Letters in an XStringSet
owl-method	OverWrite Letters in an XStringSet
parY	Get the PAR-Y Regions From a Seqinfo Object
parY-method	Get the PAR-Y Regions From a Seqinfo Object
parY-methods	Get the PAR-Y Regions From a Seqinfo Object
sjFromExons	Obtain Splice-Junctions from Exons and Transcripts
transmogrify	Mogrify a transcriptome using a set of variants
transmogrify-method	Mogrify a transcriptome using a set of variants
transmogrify-methods	Mogrify a transcriptome using a set of variants
upsetVarByCol	Show Variants by Impacted Columns
varTypes	Identify SNVs, Insertions and Deletions