chimera-package |
A package for secondary analysis of fusion products |
addGA |
Class fSet, a class represent fusion data, and methods for processing it |
addGA-method |
Class fSet, a class represent fusion data, and methods for processing it |
addRNA |
Class fSet, a class represent fusion data, and methods for processing it |
addRNA-method |
Class fSet, a class represent fusion data, and methods for processing it |
bam2fastq |
A function to extract pair end reads from the bam file generated with subreadRun function |
breakpointOverlaps |
A function to extract the reads overlapping to fusion breakpoint. |
chimera |
A package for secondary analysis of fusion products |
chimeraSeqs |
A function to generate the nucleotide sequences of a fusion event |
chimeraSeqSet |
A function to generates DNAStringSet encompassing fusion sequences |
defuseTPTN |
A function that genererate a list of fSet objects encopassing 60 experimentally validated fusions and 61 false fusions |
filterList |
A function to filter a list of fSet objects |
filterSamReads |
A function to filter SAM or BAM files |
fSet |
Class fSet, a class represent fusion data, and methods for processing it |
fSet-class |
Class fSet, a class represent fusion data, and methods for processing it |
fusionData |
Class fSet, a class represent fusion data, and methods for processing it |
fusionData-method |
Class fSet, a class represent fusion data, and methods for processing it |
fusionGA |
Class fSet, a class represent fusion data, and methods for processing it |
fusionGA-method |
Class fSet, a class represent fusion data, and methods for processing it |
fusionGRL |
Class fSet, a class represent fusion data, and methods for processing it |
fusionGRL-method |
Class fSet, a class represent fusion data, and methods for processing it |
fusionName |
A function to extract fusion names for a list of fSet object |
fusionPeptides |
A function to investigate the peptides involved in the fusion event. |
fusionRNA |
Class fSet, a class represent fusion data, and methods for processing it |
fusionRNA-method |
Class fSet, a class represent fusion data, and methods for processing it |
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 finders |
is.fSet |
A function to evaulate if an object belongs to fSet class or not |
MHmakeRandomString |
A function generating a random string |
newfSet |
A constructor for fSet class objects |
newfSet-method |
Class fSet, a class represent fusion data, and methods for processing it |
oncofuseInstallation |
A function to download oncofuse |
oncofuseRun |
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 |
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 evaluation |
subreadRun |
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 |
tophatRun |
A function to generate a bam file for fusions coverage evaluation |
validateSamFile |
A function to validate SAM or BAM files |