transmogR-package	transmogR-package
cleanVariants	cleanVariants-methods
cleanVariants,GRanges-method	cleanVariants-methods
cleanVariants,VcfFile-method	cleanVariants-methods
cleanVariants-methods	cleanVariants-methods
digestSalmon	digestSalmon
genomogrify	genomogrify-methods
genomogrify,BSgenome,GRanges-method	genomogrify-methods
genomogrify,BSgenome,VcfFile-method	genomogrify-methods
genomogrify,XStringSet,GRanges-method	genomogrify-methods
genomogrify,XStringSet,VcfFile-method	genomogrify-methods
genomogrify-methods	genomogrify-methods
indelcator	indelcator-methods
indelcator,BSgenome,GRanges-method	indelcator-methods
indelcator,DNAStringSet,GRanges-method	indelcator-methods
indelcator,XString,GRanges-method	indelcator-methods
overdispFromBoots	digestSalmon
overlapsByVar	overlapsByVar-methods
overlapsByVar,GRanges,GRanges-method	overlapsByVar-methods
overlapsByVar,GRangesList,GRanges-method	overlapsByVar-methods
overlapsByVar-methods	overlapsByVar-methods
owl	owl-methods
owl,BSgenome,GRanges-method	owl-methods
owl,XStringSet,GRanges-method	owl-methods
parY	parY-methods
parY,character-method	parY-methods
parY,Seqinfo-method	parY-methods
parY-methods	parY-methods
shiftByVar	shiftByVar
sjFromExons	sjFromExons
transmogR	transmogR-package
transmogrify	transmogrify-methods
transmogrify,BSgenome,GRanges,GRanges-method	transmogrify-methods
transmogrify,BSgenome,VcfFile,GRanges-method	transmogrify-methods
transmogrify,XStringSet,GRanges,GRanges-method	transmogrify-methods
transmogrify,XStringSet,VcfFile,GRanges-method	transmogrify-methods
transmogrify-methods	transmogrify-methods
upsetVarByCol	upsetVarByCol
varTags	varTags
varTypes	varTypes
