A package for secondary analysis of fusion products

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Documentation for package ‘chimera’ version 1.2.6

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chimera-package A package for secondary analysis of fusion products
addGA Class fSet, a class represent fusion data, and methods for processing it
addGA-method Class fSet, a class represent fusion data, and methods for processing it
addRNA Class fSet, a class represent fusion data, and methods for processing it
addRNA-method Class fSet, a class represent fusion data, and methods for processing it
chimera A package for secondary analysis of fusion products
chimeraSeqs A function to generate the nucleotide sequences of a fusion event
filterList A function to filter a list of fSet objects
fSet Class fSet, a class represent fusion data, and methods for processing it
fSet-class Class fSet, a class represent fusion data, and methods for processing it
fusionData Class fSet, a class represent fusion data, and methods for processing it
fusionData-method Class fSet, a class represent fusion data, and methods for processing it
fusionGA Class fSet, a class represent fusion data, and methods for processing it
fusionGA-method Class fSet, a class represent fusion data, and methods for processing it
fusionGRL Class fSet, a class represent fusion data, and methods for processing it
fusionGRL-method 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 associating to a fusion the peptides involved.
fusionRNA Class fSet, a class represent fusion data, and methods for processing it
fusionRNA-method Class fSet, a class represent fusion data, and methods for processing it
importFusionData A function to import fusion data detected by different fusion finders
plotCoverage A function to plot the coverage of a fusion gene
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