addNBSignificance	negbinomsig
agiFromBam	agiFromBam
AlignedGenomeIntervals	AlignedGenomeIntervals-class
AlignedGenomeIntervals-class	AlignedGenomeIntervals-class
alongChromTicks	girafe-internal
c,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
c.AlignedGenomeIntervals	AlignedGenomeIntervals-class
chrlengths	AlignedGenomeIntervals-class
chrlengths,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
chrlengths<-	AlignedGenomeIntervals-class
chrlengths<-,AlignedGenomeIntervals,numeric-method	AlignedGenomeIntervals-class
chromosome,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
chromosome,Genome_intervals-method	AlignedGenomeIntervals-class
clusters,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
clusters,Genome_intervals-method	AlignedGenomeIntervals-class
coerce,AlignedGenomeIntervals,RangedData-method	AlignedGenomeIntervals-class
coerce,AlignedRead,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
countReadsAnnotated	countReadsAnnotated
coverage,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
coverageOneStrand	girafe-internal
detail,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
estimateNBParams	negbinomsig
export	AlignedGenomeIntervals-class
export,AlignedGenomeIntervals,character,character-method	AlignedGenomeIntervals-class
export,Genome_intervals,character,ANY-method	AlignedGenomeIntervals-class
extend	AlignedGenomeIntervals-class
extend,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
extend,Genome_intervals-method	AlignedGenomeIntervals-class
extend,Genome_intervals_stranded-method	AlignedGenomeIntervals-class
featureColors	girafe-internal
fracOverlap	fracOverlap
getChromLengths	girafe-internal
getFeatureCounts	getFeatureCounts
getReadPosDf	girafe-internal
hist,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
id,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
id<-	AlignedGenomeIntervals-class
id<-,AlignedGenomeIntervals,character-method	AlignedGenomeIntervals-class
interval_included,AlignedGenomeIntervals,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
interval_included,AlignedGenomeIntervals,Genome_intervals_stranded-method	AlignedGenomeIntervals-class
interval_included,Genome_intervals_stranded,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
interval_overlap,AlignedGenomeIntervals,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
interval_overlap,AlignedGenomeIntervals,Genome_intervals-method	AlignedGenomeIntervals-class
interval_overlap,AlignedGenomeIntervals,Genome_intervals_stranded-method	AlignedGenomeIntervals-class
interval_overlap,Genome_intervals,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
interval_overlap,Genome_intervals_stranded,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
intPhred	intPhred
matches	AlignedGenomeIntervals-class
matches,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
matches<-	AlignedGenomeIntervals-class
matches<-,AlignedGenomeIntervals,integer-method	AlignedGenomeIntervals-class
medianByPosition	medianByPosition
nchar,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
newVP	girafe-internal
organism	AlignedGenomeIntervals-class
organism,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
organism<-	AlignedGenomeIntervals-class
organism<-,AlignedGenomeIntervals,character-method	AlignedGenomeIntervals-class
organism<-,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
perWindow	perWindow
plot,AlignedGenomeIntervals,ANY-method	AlignedGenomeIntervals-class
plot,AlignedGenomeIntervals,Genome_intervals_stranded-method	AlignedGenomeIntervals-class
plot,AlignedGenomeIntervals,missing-method	AlignedGenomeIntervals-class
plot,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
plotAligned	plotAligned
plotAllChrom	girafe-internal
plotAlongChromLegend	girafe-internal
plotNegBinomFit	plotnegbinomfit
plotReads	plotReads
reads	AlignedGenomeIntervals-class
reads,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
reads<-	AlignedGenomeIntervals-class
reads<-,AlignedGenomeIntervals,character-method	AlignedGenomeIntervals-class
reduce,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
reduce,CompressedIRangesList-method	reduce-extras
reduce,Genome_intervals-method	AlignedGenomeIntervals-class
reduce,IRanges-method	reduce-extras
reduce,RangedData-method	reduce-extras
reduce,Ranges-method	reduce-extras
reduce,RangesList-method	reduce-extras
reduce-methods	reduce-extras
reduceOneEnd	girafe-internal
reduceOneExact	girafe-internal
sample,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
score,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
score<-	AlignedGenomeIntervals-class
score<-,AlignedGenomeIntervals,numeric-method	AlignedGenomeIntervals-class
score<-,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
seqnames	AlignedGenomeIntervals-class
seqnames,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
show,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
sort,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
strand,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
strand<-,AlignedGenomeIntervals,factor-method	AlignedGenomeIntervals-class
strand<-,AlignedGenomeIntervals,vector-method	AlignedGenomeIntervals-class
subset	AlignedGenomeIntervals-class
subset,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
summary	AlignedGenomeIntervals-class
summary,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
trimAdapter	trimAdapter
weightedConsensusMatrix	weightedConsensusMatrix
which_nearest	whichNearestMethods
which_nearest,AlignedGenomeIntervals,Genome_intervals_stranded-method	whichNearestMethods
which_nearest,Genome_intervals,Genome_intervals-method	whichNearestMethods
which_nearest,Genome_intervals_stranded,Genome_intervals_stranded-method	whichNearestMethods
width,AlignedGenomeIntervals-method	AlignedGenomeIntervals-class
windowCountAndGC	girafe-internal
writeExportData	girafe-internal
[,AlignedGenomeIntervals,ANY,ANY-method	AlignedGenomeIntervals-class
