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chimera (version 1.12.0)

A package for secondary analysis of fusion products

Description

This package facilitates the characterisation of fusion products events. It allows to import fusion data results from the following fusion finders: chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, mapSplice, tophat-fusion, FusionMap, STAR, Rsubread, fusionCatcher.

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Version

Version

1.12.0

License

Artistic-2.0

Maintainer

Raffaele A Calogero

Last Published

February 15th, 2017

Functions in chimera (1.12.0)

chimera-package

A package for secondary analysis of fusion products

A function to generate the nucleotide sequences of a fusion event

breakpointOverlaps

A function to extract the reads overlapping to fusion breakpoint.

A function to generates DNAStringSet encompassing fusion sequences

A function to extract pair end reads from the bam file generated with subreadRun function

A function to extract fusion names for a list of fSet object

A function that genererate a list of fSet objects encopassing 60 experimentally validated fusions and 61 false fusions

A function to filter SAM or BAM files

A function to filter a list of fSet objects

Class fSet, a class represent fusion data, and methods for processing it

A function to investigate the peptides involved in the fusion event.

oncofuseInstallation

A function to download oncofuse

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

MHmakeRandomString

A function generating a random string

A function to evaulate if an object belongs to fSet class or not

gapfillerInstallation

A function to download a compiled version of GapFiller

importFusionData

A function to import fusion data detected by different fusion finders

A function to prepare files and to run gapfiller

A function to confirm fusion break point by de novo assembly

A constructor for fSet class objects

A function to generate a bam file for fusions coverage evaluation

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

removingErrorLine

A function to remove a line stopping SAM to BAM conversion

A function to represent a list of fSet as a dataframe

validateSamFile

A function to validate SAM or BAM files

A function to plot the coverage of a fusion gene

picardInstallation

A function to download picard-tools

A function to generate a bam file for fusions coverage evaluation

starInstallation

A function to download STAR

A function to extract reads info from STAR fusion output