API for girafe
Genome Intervals and Read Alignments for Functional Exploration

Global functions
.onAttach	Source code
.onLoad	Source code
.onUnload	Source code
AlignedGenomeIntervals	Man page Source code
AlignedGenomeIntervals-class	Man page
[,AlignedGenomeIntervals,ANY,ANY,ANY-method	Man page
[,AlignedGenomeIntervals,ANY,ANY-method	Man page
addNBSignificance	Man page Source code
agiFromBam	Man page Source code
agiFromOneChrBam	Source code
alongChromTicks	Man page Source code
c,AlignedGenomeIntervals-method	Man page
c.AlignedGenomeIntervals	Man page Source code
chrlengths	Man page
chrlengths,AlignedGenomeIntervals-method	Man page
chrlengths<-	Man page
chrlengths<-,AlignedGenomeIntervals,numeric-method	Man page
chromosome,AlignedGenomeIntervals-method	Man page
chromosome,Genome_intervals-method	Man page
clusters,AlignedGenomeIntervals-method	Man page
clusters,Genome_intervals-method	Man page
coerce,AlignedRead,AlignedGenomeIntervals-method	Man page
countReadsAnnotated	Man page Source code
coverage,AlignedGenomeIntervals-method	Man page
coverageOneStrand	Man page Source code
detail,AlignedGenomeIntervals-method	Man page
estimateNBParams	Man page Source code
estimatePoissonParam	Source code
export	Man page
export,AlignedGenomeIntervals,character,character-method	Man page
export,Genome_intervals,character,ANY-method	Man page
extend	Man page
extend,AlignedGenomeIntervals-method	Man page
extend,Genome_intervals-method	Man page
extend,Genome_intervals_stranded-method	Man page
featureColors	Man page Source code
fracOverlap	Man page Source code
getChromLengths	Man page Source code
getFeatureCounts	Man page Source code
getReadPosDf	Man page Source code
hist,AlignedGenomeIntervals-method	Man page
id,AlignedGenomeIntervals-method	Man page
id<-	Man page
id<-,AlignedGenomeIntervals,character-method	Man page
intPhred	Man page Source code
interval_included,AlignedGenomeIntervals,AlignedGenomeIntervals-	Man page
interval_included,AlignedGenomeIntervals,Genome_intervals_strand	Man page
interval_included,Genome_intervals_stranded,AlignedGenomeInterva	Man page
interval_overlap,AlignedGenomeIntervals,AlignedGenomeIntervals-m	Man page
interval_overlap,AlignedGenomeIntervals,Genome_intervals-method	Man page
interval_overlap,AlignedGenomeIntervals,Genome_intervals_strande	Man page
interval_overlap,Genome_intervals,AlignedGenomeIntervals-method	Man page
interval_overlap,Genome_intervals_stranded,AlignedGenomeInterval	Man page
matches	Man page
matches,AlignedGenomeIntervals-method	Man page
matches<-	Man page
matches<-,AlignedGenomeIntervals,integer-method	Man page
medianByPosition	Man page Source code
nchar,AlignedGenomeIntervals-method	Man page
newAGIoverlap	Source code
newVP	Man page Source code
oldAGIoverlap	Source code
organism	Man page
organism,AlignedGenomeIntervals-method	Man page
organism<-	Man page
organism<-,AlignedGenomeIntervals,character-method	Man page
organism<-,AlignedGenomeIntervals-method	Man page
perWindow	Man page Source code
plot,AlignedGenomeIntervals,ANY-method	Man page
plot,AlignedGenomeIntervals,Genome_intervals_stranded-method	Man page
plot,AlignedGenomeIntervals,missing-method	Man page
plot,AlignedGenomeIntervals-method	Man page
plotAligned	Man page Source code
plotAllChrom	Man page Source code
plotAlongChromLegend	Man page Source code
plotFeatures	Source code
plotNegBinomFit	Man page Source code
plotReads	Man page Source code
reads	Man page
reads,AlignedGenomeIntervals-method	Man page
reads<-	Man page
reads<-,AlignedGenomeIntervals,character-method	Man page
reduce,AlignedGenomeIntervals-method	Man page
reduce,CompressedIRangesList-method	Man page
reduce,Genome_intervals-method	Man page
reduce,IRanges-method	Man page
reduce,IntegerRanges-method	Man page
reduce,IntegerRangesList-method	Man page
reduce-methods	Man page
reduceOne	Source code
reduceOneEnd	Man page Source code
reduceOneExact	Man page Source code
sample,AlignedGenomeIntervals-method	Man page
score,AlignedGenomeIntervals-method	Man page
score<-	Man page
score<-,AlignedGenomeIntervals,numeric-method	Man page
score<-,AlignedGenomeIntervals-method	Man page
seqnames	Man page
seqnames,AlignedGenomeIntervals-method	Man page
show,AlignedGenomeIntervals-method	Man page
sort,AlignedGenomeIntervals-method	Man page
strand,AlignedGenomeIntervals-method	Man page
strand<-,AlignedGenomeIntervals,factor-method	Man page
strand<-,AlignedGenomeIntervals,vector-method	Man page
subset	Man page
subset,AlignedGenomeIntervals-method	Man page
summary	Man page
summary,AlignedGenomeIntervals-method	Man page
trimAdapter	Man page Source code
weightedConsensusMatrix	Man page Source code
which_nearest	Man page
which_nearest,AlignedGenomeIntervals,Genome_intervals_stranded-m	Man page
which_nearest,Genome_intervals,Genome_intervals-method	Man page
which_nearest,Genome_intervals_stranded,Genome_intervals_strande	Man page
width,AlignedGenomeIntervals-method	Man page
windowCountAndGC	Man page Source code
writeExportData	Man page Source code