API for girafe
Genome Intervals and Read Alignments for Functional Exploration

Global functions
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
onAttach Source code
onLoad Source code
onUnload 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
girafe documentation built on May 2, 2018, 2:44 a.m.