Man pages for Bioconductor-mirror/chimera
A package for secondary analysis of fusion products

bam2fastqA function to extract pair end reads from the bam file...
breakpointOverlapsA function to extract the reads overlapping to fusion...
chimera-packageA package for secondary analysis of fusion products
chimeraSeqsA function to generate the nucleotide sequences of a fusion...
chimeraSeqSetA function to generates DNAStringSet encompassing fusion...
class.fSetClass fSet, a class represent fusion data, and methods for...
defuseTPTNA function that genererate a list of fSet objects encopassing...
filterListA function to filter a list of fSet objects
filterSamReadsA function to filter SAM or BAM files
fusionNameA function to extract fusion names for a list of fSet object
fusionPeptidesA function to investigate the peptides involved in the fusion...
gapfillerInstallationA function to download a compiled version of GapFiller
gapfillerRunA function to confirm fusion break point by de novo assembly
gapfillerWrapA function to prepare files and to run gapfiller
importFusionDataA function to import fusion data detected by different fusion...
is.fSetA function to evaulate if an object belongs to fSet class or...
MHmakeRandomStringA function generating a random string
newfSetA constructor for fSet class objects
oncofuseInstallationA function to download oncofuse
oncofuseRunA function to annotate fusions with Oncofuse. Oncofuse is a...
picardInstallationA function to download picard-tools
plotCoverageA function to plot the coverage of a fusion gene
prettyPrintA function to represent a list of fSet as a dataframe
removingErrorLineA function to remove a line stopping SAM to BAM conversion
starInstallationA function to download STAR
starReadsA function to extract reads info from STAR fusion output
starRunA function to generate a bam file for fusions coverage...
subreadRunA function to generate a bam file for fusions coverage...
supportingReadsA function to extract supporting reads values from a list of...
tophatInstallationA function to download tophat, bowtie and samtools
tophatRunA function to generate a bam file for fusions coverage...
validateSamFileA function to validate SAM or BAM files
Bioconductor-mirror/chimera documentation built on June 1, 2017, 5:30 a.m.