chimera: A package for secondary analysis of fusion products

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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.

Author
Raffaele A Calogero, Matteo Carrara, Marco Beccuti, Francesca Cordero
Date of publication
None
Maintainer
Raffaele A Calogero <raffaele.calogero@unito.it>
License
Artistic-2.0
Version
1.16.0

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

Files in this package

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