aa	Proteins-class
aa,Proteins-method	Proteins-class
acols	Proteins-class
addIdentificationData,Proteins,character-method	Proteins-class
addPeptideFragments	Proteins-class
addPeptideFragments,Proteins,character-method	Proteins-class
avarLabels	Proteins-class
avarLabels,Proteins-method	Proteins-class
calculateHeavyLabels	calculateHeavyLabels
class:Proteins	Proteins-class
cleave,Proteins-method	Proteins-class
etrid2grl	etrid2grl
isCleaved	Proteins-class
isForward	isReverse
isReverse	isReverse
length,Proteins-method	Proteins-class
mapToGenome	coordinate-mapping-methods
mapToGenome,ANY,ANY-method	coordinate-mapping-methods
mapToGenome,Proteins,EnsDb-method	coordinate-mapping-methods
mapToGenome,Proteins,GRangesList-method	coordinate-mapping-methods
mapToGenome-methods	coordinate-mapping-methods
metadata,Proteins-method	Proteins-class
metadata<-,Proteins-method	Proteins-class
names,Proteins-method	Proteins-class
p	p
pcols	Proteins-class
pfeatures	Proteins-class
pfeatures,Proteins-method	Proteins-class
pfilter	Proteins-class
pfilter,Proteins-method	Proteins-class
plot,Proteins,missing-method	Proteins-class
plotAsAnnotationTrack	plotAsAnnotationTrack
plotAsGeneRegionTrack	plotAsAnnotationTrack
pmapToGenome	coordinate-mapping-methods
pmapToGenome,ANY,ANY-method	coordinate-mapping-methods
pmapToGenome,Proteins,GRangesList-method	coordinate-mapping-methods
pmapToGenome-methods	coordinate-mapping-methods
pms	p
Pparams	Pparams-class
Pparams-class	Pparams-class
pranges	Proteins-class
pranges,Proteins-method	Proteins-class
pranges<-	Proteins-class
pranges<-,Proteins,CompressedIRangesList-method	Proteins-class
proteinCoding	proteinCoding-methods
proteinCoding,GRanges-method	proteinCoding-methods
proteinCoding,GRangesList-method	proteinCoding-methods
proteinCoding-methods	proteinCoding-methods
proteinCoverage	Proteins-class
Proteins	Proteins-class
Proteins,character,missing-method	Proteins-class
Proteins,EnsDb,missing-method	Proteins-class
Proteins,missing,character-method	Proteins-class
Proteins,missing,missing-method	Proteins-class
Proteins-class	Proteins-class
proteotypic	Proteins-class
pvarLabels	Proteins-class
pvarLabels,Proteins-method	Proteins-class
rmEmptyRanges	Proteins-class
seqnames,Proteins-method	Proteins-class
show,Pparams-method	Pparams-class
show,Proteins-method	Proteins-class
[,Proteins,ANY,ANY,ANY-method	Proteins-class
[,Proteins,ANY,ANY-method	Proteins-class
[[,Proteins,ANY,ANY-method	Proteins-class
