A function that genererate a list of fSet objects encopassing 60 experimentally validated fusions and 61 false fusions
A function to filter a list of fSet objects
A function to investigate the peptides involved in the fusion event.
A function to download a compiled version of GapFiller
A package for secondary analysis of fusion products
A constructor for fSet class objects
A function generating a random string
A function to generate the nucleotide sequences of a fusion event
A function to download STAR
A function to extract reads info from STAR fusion output
A function to represent a list of fSet as a dataframe
A function to remove a line stopping SAM to BAM conversion
A function to extract pair end reads from the bam file generated with subreadRun function
A function to extract the reads overlapping to fusion breakpoint.
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
A function to download oncofuse
A function to extract supporting reads values from a list of fSet object
A function to download tophat, bowtie and samtools
A function to generate a bam file for fusions coverage evaluation
A function to validate SAM or BAM files
A function to generates DNAStringSet encompassing fusion sequences
A function to import fusion data detected by different fusion finders
Class fSet, a class represent fusion data, and methods for
processing it
A function to download picard-tools
A function to evaulate if an object belongs to fSet class or not
A function to plot the coverage of a fusion gene
A function to filter SAM or BAM files
A function to extract fusion names for a list of fSet object
A function to confirm fusion break point by de novo assembly
A function to prepare files and to run gapfiller
A function to generate a bam file for fusions coverage evaluation
A function to generate a bam file for fusions coverage evaluation