chimera: A package for secondary analysis of fusion products

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("chimera")
AuthorRaffaele A Calogero, Matteo Carrara, Marco Beccuti, Francesca Cordero
Bioconductor views Infrastructure
Date of publicationNone
MaintainerRaffaele A Calogero <raffaele.calogero@unito.it>
LicenseArtistic-2.0
Version1.18.0

View on Bioconductor

Man pages

bam2fastq: A function to extract pair end reads from the bam file...

breakpointOverlaps: A function to extract the reads overlapping to fusion...

chimera-package: A package for secondary analysis of fusion products

chimeraSeqs: A function to generate the nucleotide sequences of a fusion...

chimeraSeqSet: A function to generates DNAStringSet encompassing fusion...

class.fSet: Class fSet, a class represent fusion data, and methods for...

defuseTPTN: A function that genererate a list of fSet objects encopassing...

filterList: A function to filter a list of fSet objects

filterSamReads: A function to filter SAM or BAM files

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

fusionPeptides: A function to investigate the peptides involved in the fusion...

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...

is.fSet: A function to evaulate if an object belongs to fSet class or...

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...

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...

subreadRun: A function to generate a bam file for fusions coverage...

supportingReads: A function to extract supporting reads values from a list of...

tophatInstallation: A function to download tophat, bowtie and samtools

tophatRun: A function to generate a bam file for fusions coverage...

validateSamFile: A function to validate SAM or BAM files

Functions

addGA Man page
addGA,fSet-method Man page
addRNA Man page
addRNA,fSet-method Man page
bam2fastq Man page
breakpointOverlaps Man page
chimera Man page
chimera-package Man page
chimeraSeqs Man page
chimeraSeqSet Man page
defuseTPTN Man page
filterList Man page
filterSamReads Man page
fSet Man page
fSet-class Man page
fusionData Man page
fusionData,fSet-method Man page
fusionGA Man page
fusionGA,fSet-method Man page
fusionGRL Man page
fusionGRL,fSet-method Man page
fusionName Man page
fusionPeptides Man page
fusionRNA Man page
fusionRNA,fSet-method Man page
gapfillerInstallation Man page
gapfillerRun Man page
gapfillerWrap Man page
importFusionData Man page
is.fSet Man page
MHmakeRandomString Man page
newfSet Man page
newfSet,fSet-method Man page
oncofuseInstallation Man page
oncofuseRun Man page
picardInstallation Man page
plotCoverage Man page
prettyPrint Man page
removingErrorLine Man page
starInstallation Man page
starReads Man page
starRun Man page
subreadRun Man page
supportingReads Man page
tophatInstallation Man page
tophatRun Man page
validateSamFile Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/AllGenerics.R R/AllUtilities.R R/addGA.R R/addRNA.R R/chimeraSeqs.R R/defuseTPTN.R R/denovoFusionCheck.R R/fusionData.R R/fusionGA.R R/fusionGRL.R R/fusionPeptides.R R/fusionRNA.R R/importFusionData.R R/is.fSet.R R/plotCoverage.R R/show.R R/star.R R/subread.R R/tophat.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/chimera.R
inst/doc/chimera.Rnw
inst/doc/chimera.pdf
inst/examples
inst/examples/Edgreen_fm.txt
inst/examples/Edgren_cs.txt
inst/examples/Edgren_df.tsv
inst/examples/Edgren_true.positives.txt
inst/examples/SULF2_ARFGEF2.fa
inst/examples/defuse_TP_FP.txt
inst/examples/edgren.stat.detection.txt
inst/examples/fset_ARFGEF2-SULF2.rda
inst/examples/mcf7.FMFusionReport
inst/examples/mcf7_sample_1.fq
inst/examples/mcf7_sample_2.fq
inst/examples/mcf7_trs_accepted_hits.bam
inst/examples/uc002xtx.4-272_uc010zyd.2-988.fa
inst/examples/uc002xtx.4-272_uc010zyd.2-988_R1.fastq
inst/examples/uc002xtx.4-272_uc010zyd.2-988_R2.fastq
inst/examples/uc002xvp.1-243_uc002iyu.4-1031.fa
inst/examples/uc002xvp.1-243_uc002iyu.4-1031_R1.fastq
inst/examples/uc002xvp.1-243_uc002iyu.4-1031_R2.fastq
man
man/MHmakeRandomString.Rd man/bam2fastq.Rd man/breakpointOverlaps.Rd man/chimera-package.Rd man/chimeraSeqSet.Rd man/chimeraSeqs.Rd man/class.fSet.Rd man/defuseTPTN.Rd man/filterList.Rd man/filterSamReads.Rd man/fusionName.Rd man/fusionPeptides.Rd man/gapfillerInstallation.Rd man/gapfillerRun.Rd man/gapfillerWrap.Rd man/importFusionData.Rd man/is.fSet.Rd man/newfSet.Rd man/oncofuseInstallation.Rd man/oncofuseRun.Rd man/picardInstallation.Rd man/plotCoverage.Rd man/prettyPrint.Rd man/removingErrorLine.Rd man/starInstallation.Rd man/starReads.Rd man/starRun.Rd man/subreadRun.Rd man/supportingReads.Rd man/tophatInstallation.Rd man/tophatRun.Rd man/validateSamFile.Rd
src
src/StarParser.cpp
src/general.h
vignettes
vignettes/chimera.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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