Man pages for girafe
Genome Intervals and Read Alignments for Functional Exploration

agiFromBamCreate AlignedGenomeIntervals objects from BAM files.
AlignedGenomeIntervals-classClass 'AlignedGenomeIntervals'
countReadsAnnotatedSum up aligned reads per category of genome feature
fracOverlapRetrieve intervals overlapping by fraction of width
getFeatureCountsget the read counts for a supplied set of genomic features
girafe-internalInternal girafe functions
intPhredExtract integer Phred score values from FastQ data
medianByPositionCompute median quality for each nucleotide position
negbinomsigassess significance of sliding-window read counts
perWindowInvestigate aligned reads in genome intervals with sliding...
plotAlignedVisualise reads aligned to genome intervals
plotnegbinomfitPlot Negative Binomial Fit
plotReadsFunction to plot aligned reads along the chromosome
reduce-extrasAuxiliary methods for Function reduce in Package 'girafe'
trimAdapterRemove 3' adapter contamination
weightedConsensusMatrixcompute weighted consensus matrix
whichNearestMethodsMethods for function 'which_nearest' and genome intervals
girafe documentation built on Oct. 31, 2019, 3:20 a.m.