bam2fastq               A function to extract pair end reads from the
                        bam file generated with subreadRun function
breakpointOverlaps      A function to extract the reads overlapping to
                        fusion breakpoint.
chimera-package         A package for secondary analysis of fusion
                        products
chimeraSeqs             A function to generate the nucleotide sequences
                        of a fusion event
chimeraSeqSet           A function to generates DNAStringSet
                        encompassing fusion sequences
defuseTPTN              A function that genererate a list of fSet
                        objects encopassing 60 experimentally validated
                        fusions and 61 false fusions
filterList              A function to filter a list of fSet objects
filterSamReads          A function to filter SAM or BAM files
fSet                    Class fSet, a class represent fusion data, and
                        methods for processing it
fusionName              A function to extract fusion names for a list
                        of fSet object
fusionPeptides          A function to investigate the peptides involved
                        in the fusion event.
gapfillerInstallation   A function to download a compiled version of
                        GapFiller
gapfillerRun            A function to confirm fusion break point by de
                        novo assembly
gapfillerWrap           A function to prepare files and to run
                        gapfiller
importFusionData        A function to import fusion data detected by
                        different fusion finders
is.fSet                 A function to evaulate if an object belongs to
                        fSet class or not
MHmakeRandomString      A function generating a random string
newfSet                 A constructor for fSet class objects
oncofuseInstallation    A function to download oncofuse
oncofuseRun             A function to annotate fusions with Oncofuse.
                        Oncofuse is a naive bayesian classifier. Its
                        goal is to identify those fusion sequences with
                        higher probability of being driver than
                        passenger events
picardInstallation      A function to download picard-tools
plotCoverage            A function to plot the coverage of a fusion
                        gene
prettyPrint             A function to represent a list of fSet as a
                        dataframe
removingErrorLine       A function to remove a line stopping SAM to BAM
                        conversion
starInstallation        A function to download STAR
starReads               A function to extract reads info from STAR
                        fusion output
starRun                 A function to generate a bam file for fusions
                        coverage evaluation
subreadRun              A function to generate a bam file for fusions
                        coverage evaluation
supportingReads         A function to extract supporting reads values
                        from a list of fSet object
tophatInstallation      A function to download tophat, bowtie and
                        samtools
tophatRun               A function to generate a bam file for fusions
                        coverage evaluation
validateSamFile         A function to validate SAM or BAM files
