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.

AuthorRaffaele A Calogero, Matteo Carrara, Marco Beccuti, Francesca Cordero
Date of publicationNone
MaintainerRaffaele A Calogero <raffaele.calogero@unito.it>
LicenseArtistic-2.0
Version1.16.0

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

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

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