cancer-genomics/trellis
Somatic structural variant analysis

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Search the cancer-genomics/trellis package
Functions
1056
Source code
123
Man pages
187
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cancer-genomics/trellis: Somatic structural variant analysis
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API

API for cancer-genomics/trellis
Somatic structural variant analysis

Global functions
"Transcripts", Man page
$,RearrangementList,ANY-method Man page
$,RearrangementList-method Man page
$<-,RearrangementList-method Man page
, Man page
.GAlignmentPairs Man page Source code
.add_mcols Source code
.each_block_granges Source code
.empty_filters Source code
.expand Source code
.fusionTable Source code
.fusion_GRangesList Source code
.gc_model Source code
.getFusedTx Source code
.getReadSeqsForDeletion Source code
.getReadSeqsForRear Source code
.ggRearrange Source code
.ggRearrange_sequences Source code
.hemizygousBorders Source code
.hits Source code
.hits_intersection Source code
.hits_union Source code
.homozygousBorders Source code
.invalid_split_reads Source code
.isFirstSegment.GAlignments Source code
.isFirstSegment.integer Source code
.isFirstSegment.matrix Source code
.isInFrame Source code
.isLastSegment.GAlignments Source code
.isLastSegment.integer Source code
.isLastSegment.matrix Source code
.listTagsByGroup Source code
.list_fusion_data Source code
.mappedReadPairFlags Source code
.match_index_variant Source code Source code Source code
.merge_partial_overlap Source code
.organize_reads Source code
.organize_with_split_reads Source code
.organize_without_split_reads Source code
.query_bam Source code
.rear_DataFrame Source code
.reviseEachJunction Source code
.safelyChangeEnd Source code
.safelyChangeStart Source code
.scan_all_readpairs Source code
.segment Source code
.segmentBins Source code
.select_junction Source code
.seqdataframe Source code
.splitread_intersection Source code
.trimInvalidReads Source code
.trimInvalidReadsGAlign Source code
.trim_one_base Source code
.writefasta Source code
AmpliconGraph Man page Source code
AmpliconGraph-class Man page
AnchoredReadPairs Source code
ClippedTranscripts Man page
ClippedTranscripts,missing,missing-method Man page
ClippedTranscripts-class Man page
DNAcopy Man page
DNAcopy-class Man page
DeletionList Man page
DeletionList,GRangesList-method Man page
DeletionList,list-method Man page
DeletionList,missing-method Man page
DeletionParam Man page Source code
DeletionParam-class Man page
ExonSubset Man page Source code
ExonSubset-class Man page
ExonSubset-method Man page
FilterEdgeParam Source code
PreprocessViews2 Man page Source code
PreprocessViews2-class Man page
R1isFirst Source code
R1lessR2 Source code
R1pos Source code
R1strand Source code
R2neg Source code
R2strand Source code
Rearrangement Man page Source code
Rearrangement-class Man page
RearrangementList Man page
RearrangementList, Man page
RearrangementList,Rearrangement-method Man page
RearrangementList,list-method Man page
RearrangementList,missing-method Man page
RearrangementList-class Man page
RearrangementParams Man page Source code Source code
RearrangementParams-class Man page
SVFilters Source code
SegmentParam Man page Source code
SegmentParam-class Man page
StructuralVariant Man page Source code
StructuralVariant-class Man page
Transcripts Man page Source code
Transcripts-class Man page
TranscriptsFusion Man page Source code
TranscriptsFusion-class Man page
[,Rearrangement,ANY,ANY,ANY-method Man page
[,RearrangementList,ANY,ANY,ANY-method Man page
[,StructuralVariant,ANY,ANY,ANY-method Man page
[,StructuralVariant,ANY,ANY-method Man page
[,StructuralVariant,numeric,ANY,ANY-method Man page
[,StructuralVariant,numeric,ANY-method Man page
[,TranscriptsFusion,ExonSubset,ANY,ANY-method Man page
[[,RearrangementList,ANY,ANY-method Man page
[[,StructuralVariant,ANY,ANY-method Man page
[[,Transcripts,ANY,ANY-method Man page
[[<-,RearrangementList,ANY,ANY,ANY-method Man page
[[<-,Transcripts,ANY,ANY,GRangesList-method Man page
aaFivePrime Source code
aaJunction Source code
aaThreePrime Source code
aaThreePrime_list Source code
aa_granges Man page Source code
aberrantSep Man page Source code
acf2 Man page Source code
add.info Man page Source code
addDuplications Source code
addFlanks Source code
addFocalDupsFlankingAmplicon Man page Source code
addNode,character,AmpliconGraph,ANY-method Man page
addNode,character,AmpliconGraph-method Man page
addVariant Source code
addVariant2 Source code
addXCoordinateForTag Source code
add_amplicons Source code
add_amplicons_bedops Source code
add_amplicons_bedops2 Source code
adjudicateHemizygousOverlap Source code
adjudicateHemizygousOverlap2 Source code
adjudicateHomozygousOverlap Source code
adjudicateHomozygousOverlap2 Source code
adjustBinSizeByLinkedTagPairs Source code
adjustLeftBinSize Source code
adjustRightBinSize Source code
allGapsInReadPairs Source code
allProperReadPairs Source code
allProperReadPairs_bedops Source code
allProperReadPairs_bedops1 Source code
allProperReadPairs_bedops2 Source code
ampliconFilters Source code
ampliconNames Man page Source code
ampliconParams Man page Source code
ampliconQueryRanges Source code
ampliconRanges Man page
ampliconRanges,AmpliconGraph-method Man page
ampliconRanges,GRanges-method Man page
ampliconRanges<- Man page
ampliconRanges<-,AmpliconGraph-method Man page
amplicon_graph Man page
amplicons Man page
amplicons,AmpliconGraph-method Man page
amplicons-data Man page
amplicons<- Man page
amplicons<-,AmpliconGraph,ANY-method Man page
amplicons<-,AmpliconGraph-method Man page
amplified_segments Source code
annotate3prime Source code
annotate5prime Source code
annotateBlatRecords Man page Source code
annotateRPsWithLinkId Source code
annotateRecurrent Man page Source code
annotateSide Source code
annotate_amplicons Source code
anyLengthZero Source code
anyPromoter Source code
applyFilters Source code
arrange_clipped_tx Source code
as Man page
assays,PreprocessViews2-method Man page
assemblyGaps Man page
assemblyGaps,AmpliconGraph-method Man page
assemblyGaps<-,AmpliconGraph,ANY-method Man page
atLeastOneTagMapsToCluster Source code
autosomeNames Man page
autosomeNames,BamViews-method Man page
autosomeNames,GRanges-method Man page
axis_labels3p Source code
axis_labels5p Source code
axis_limit3p Source code
axis_limit5p Source code
axis_limits Source code
backgroundChr Source code
backgroundChunk Source code
backgroundCorrect Source code
backgroundSample Source code
bamSeqLevelsStyle Man page Source code
basepairJunction Source code
bed2gr Source code
binFragments Man page Source code
binGCCorrect Man page Source code
binMedians Man page Source code
binNormalize Man page Source code
binnedCounts Man page Source code
blatBlockList Source code
blatGRanges Source code
blatGRanges2 Source code
blatScores Man page Source code
blatStartList Source code
blat_to_granges Source code
blat_unmapped Man page
borderSize Source code
bothGenesInUniprot Source code
bothLengthZero Source code
bothTagsMapToCluster Source code
bp_breaks Source code
bp_trans Source code
breakpointInvA Source code
breakpointInvB Source code
breakpointsForQuery Source code
breakpointsInversion Source code
c,RearrangementList-method Man page
c-method Man page
calcAlleleFreq Source code
callOverlappingHemizygous Source code
calls Man page
calls,StructuralVariant,ANY-method Man page
calls,StructuralVariant-method Man page
calls<- Man page
calls<-,StructuralVariant-method Man page
candidateFusions Source code
candidateSplitRead Source code
cbs2granges Man page Source code
cbs_alpha Man page
cbs_alpha,SegmentParam-method Man page
cgov44t_preprocess Source code
charstrand Source code
checkHemizygousSpanningHomozygous Source code
checkMcols Source code
check_splitreads Source code
chrYMedians Source code
chromosome Man page
chromosome,GAlignments-method Man page
chromosome,GRanges-method Man page
chromosome,RangedSummarizedExperiment-method Man page
chromosome,StructuralVariant-method Man page
chunkseq Source code
clip Man page Source code
clip3prime Source code
clip5prime Source code
clipFivePrime Source code
clipFivePrimeJunctions Source code
clipThreePrime Source code
clippedProtein Source code
clusterRegions Source code
clusterTags Source code
codingJunctions Man page Source code
codonMultiple Source code
coerce,PreprocessViews2,RangedSummarizedExperiment-method Man page
colData,RearrangementList,ANY-method Man page
colData,RearrangementList-method Man page
colData<-,RearrangementList,ANY-method Man page
computeFractionLinkingTags Source code
conciseGRangeSummary Source code
copynumber Man page
copynumber,RangedSummarizedExperiment-method Man page
copynumber,StructuralVariant-method Man page
copynumber<- Man page
copynumber<-,RangedSummarizedExperiment,matrix-method Man page
copynumber<-,StructuralVariant,ANY-method Man page
countParam Man page Source code
countReads2 Man page
cstrand Source code Source code
deletion Man page
deletion_call Man page Source code
deletions Man page
deletions2 Man page
divisibleBy3Seq Source code
dnaSeqLengths Source code
driver Man page
driver,AmpliconGraph-method Man page
driver_genes Source code
dropDuplicatedQueryHits Source code
dropRearNearDeletion Source code
dt2ga2 Man page Source code
duplicatedGAlignmentPairs Man page Source code
eachBlockAsGRanges Source code
edgeFilters Source code
edgeStats Source code
edges,AmpliconGraph-method Man page
elementType,RearrangementList-method Man page
empty_record Source code
endAmpliconBoundary Source code
endSeqAtCodon Source code
evaluateContext Source code
exonTracks2 Source code
exonsByTx Source code
expand.grid2 Source code
expandGRanges Man page Source code
extractTranscriptSeqs2 Source code
fTable2 Source code
fastaFiles Source code
fasta_unmapped Man page Source code
fillInMissing Source code
filterBy Man page
filterBy,GRanges,GRanges-method Man page
filterGermlineRear Man page Source code
filterGermlineRearList Man page Source code
filterPairedReads Man page Source code
filterRear Man page Source code
filterRearExperiment Man page Source code
filterRearrangementList Man page Source code
filterRearrangementList2 Source code
filterSNPs Source code
filterSmallAmplicons Source code
filterTagClusters Source code
finalize_deletions Source code
finalize_deletions_bedops Source code
finalize_deletions_bedops1 Source code
finalize_deletions_bedops2 Source code
findCandidates2 Man page Source code
findSpanningHemizygousDeletion Source code
firstIsLeft Source code
fit_models_sequentially Source code
fivePrimeTranscriptNames Source code
fiveTo3List Man page Source code
fiveTo3Prime Man page
fiveTo3PrimeList Source code
flankingDuplications Source code
flankingRanges Source code
focalAmpliconDupRanges Man page Source code
fractionLinkingTags Man page
fractionLinkingTags,Rearrangement,ANY-method Man page
fractionLinkingTags,Rearrangement-method Man page
fractionLinkingTags,RearrangementList-method Man page
fractionLinkingTags<- Man page
fractionLinkingTags<-,Rearrangement-method Man page
frame Source code
fullTranscripts Man page Source code
function(object) Man page
fuse Man page
fuse,ClippedTranscripts-method Man page
fuse,TranscriptsFusion-method Man page
fuseCDS Source code
fuseCDS_Rlist Man page Source code
fuseExonTracks Source code
fuseExonTracksPM Source code
fuseProteinTracks Source code
fusionList Man page Source code
fusionNames Man page
fusionNames,TranscriptsFusion-method Man page
fusionTable Man page Source code
fusionTable2 Man page Source code
fusion_CDS Source code
fusions Man page
fusions,TranscriptsFusion,list-method Man page
fusions,TranscriptsFusion-method Man page
fusions<- Man page
fusions<-,TranscriptsFusion,list-method Man page
ga2gr Man page Source code
ga2tibble_first Source code
ga2tibble_last Source code
gapBetweenLowCopyRanges Source code
gapToGRanges Source code
gaps0 Source code
gapsInHemiDel Source code
geneParams Source code
genes Source code
genomeAndBlatOverlap Source code
genomeFilters Source code
genomeGRanges Source code
germline Source code
germlineCNV Source code
germlineFilters Man page Source code
germlineOutliers Man page Source code
getBamView Source code
getCDFun Source code
getCDS Man page Source code
getDrivers Source code
getExonsAmp2_4 Source code
getExonsDel1_2 Source code
getExonsInversion1_2 Source code
getExonsInversion3_4 Source code
getExonsInversionBalanced Source code
getExonsTranslocationBalanced Source code
getGenes Source code
getImproperAlignmentPairs Man page Source code
getProperAlignmentPairs Man page Source code
getScale Man page Source code
getSequenceOfReads Man page
getSequenceOfReads,Rearrangement-method Man page
getSequenceOfReads,RearrangementList-method Man page
getSequenceOfReads,StructuralVariant-method Man page
getSequenceOfReads_bedops Man page Source code
get_improper_readpairs Man page Source code
get_improper_readpairs2 Source code
get_readpairs Man page Source code
get_readpairs2 Man page Source code
get_readpairs2_bedops Source code
get_readpairs2_bedops2 Source code
get_rearrangement_id Source code
ggRearrange Man page Source code
ggRearrange2 Source code
ggRearrangeLegend Source code
granges_copynumber Man page Source code
granges_copynumber2 Source code
graph Man page
graph,AmpliconGraph,ANY-method Man page
graph,AmpliconGraph-class Man page
graph,AmpliconGraph-method Man page
graph<- Man page
graph<-,AmpliconGraph-method Man page
grlapply Source code
groupAmplicons Man page Source code
groupSVs Source code
groupedVariant Man page
groupedVariant,StructuralVariant,ANY-method Man page
groupedVariant,StructuralVariant-method Man page
groupedVariant<- Man page
groupedVariant<-,StructuralVariant-method Man page
harmonizeReadMcols Source code
hemizygousBorders Source code
hemizygousThr Man page Source code
hgnc Source code
hitsWithDifferentTargets Source code
hitsWithSameQuery Source code
homozygousBorders Source code
homozygousThr Man page Source code
identicalReadQueries Source code
identifier Man page
identifier,Transcripts,ANY-methodsetMethod("identifier", Man page
identifier,Transcripts-method Man page
identifier<- Man page
identifier<-,Transcripts-method Man page
import_mum_bedops Source code
improper Man page
improper,Rearrangement,GAlignmentPairs-method Man page
improper,Rearrangement-method Man page
improper,StructuralVariant,GAlignmentPairs-method Man page
improper,StructuralVariant-method Man page
improper.path Source code
improper<- Man page
improper<-,Rearrangement,GAlignmentPairs-method Man page
improper<-,StructuralVariant,GAlignmentPairs-method Man page
improperAlignmentFlags Man page Source code
improperAlignmentParams Man page Source code
improperRP Source code
improperSides Source code
inFrameFusions Man page Source code
inFrameList Man page Source code
inFrameNoStop Man page Source code
inRearrangement.left Man page
inRearrangement.left,ExonSubset-method Man page
inRearrangement.right Man page
inRearrangement.right,ExonSubset-method Man page
indexImproper Man page
indexImproper,StructuralVariant,list-method Man page
indexImproper,StructuralVariant-method Man page
indexImproper<- Man page
indexImproper<-,StructuralVariant,list-method Man page
indexProper Man page
indexProper,StructuralVariant,list-method Man page
indexProper,StructuralVariant-method Man page
indexProper<- Man page
indexProper<-,StructuralVariant,list-method Man page
indexRanges Man page
indexRanges,PreprocessViews2-method Man page
indexRanges<- Man page
indexRanges<-,PreprocessViews2-method Man page
inflectionFun Source code
initializeImproperIndex Source code
initializeImproperIndex2 Source code Source code
initializeImproperIndex3 Source code
initializeProperIndex2 Source code
initializeProperIndex3 Source code
initialize_graph Source code
initialize_graph2 Source code
intOverWidth Man page Source code
integer_vector Source code
intersectionAligned Man page Source code
isAmplicon Man page
isAmplicon,AmpliconGraph-method Man page
isAmplicon,GRanges-method Man page
isComplex Man page
isDuplicate Man page Source code
isDuplication Source code
isFusion Source code
isGap Source code
isHemizygousDeletion Source code
isInFrame Source code
isInFrame_oneframe Source code
isLargeHemizygous Source code
isNegStrand Source code
isNotAmplicon Source code
isNotGermline Man page Source code
isOutlier Source code
isSomatic Man page
isSomatic,GRanges-method Man page
isTranslocation Source code
is_3pTumor_sameAs_3pRef Source code
is_invalid_splits Source code
is_valid_proper_index Source code
is_valid_splits Man page Source code
iscnName Source code
joinNearGRanges Man page Source code
kb_trans Source code
labelGeneName Source code
label_orientation Source code
lapply,RearrangementList-method Man page
lapply,StructuralVariant-method Man page
left Man page
left,ClippedTranscripts-method Man page
leftAlwaysFirst Source code
leftHemizygousHomolog Source code
length,AmpliconGraph-method Man page
length,Rearrangement-method Man page
length,RearrangementList-method Man page
length,StructuralVariant-method Man page
link1id Source code
link2id Source code
linkAmplicons Source code
linkClustersByReadPairs Source code
linkFocalDups Source code
linkNearAmplicons Source code
link_amplicons Source code
linkedBins Man page
linkedBins,Rearrangement,ANY-method Man page
linkedBins,Rearrangement-method Man page
linkedBins,RearrangementList,ANY-method Man page
linkedBins,RearrangementList-method Man page
linkedBins<- Man page
linkedBins<-,Rearrangement-method Man page
linkedBins<-,RearrangementList-method Man page
linkedDuplicatedRanges Source code
linkedTo Man page
linkedTo,GRanges-method Man page
linkedTo,Rearrangement-method Man page
linkedTo,RearrangementList-method Man page
listCNVs Man page Source code
listDeletions Man page Source code
listFusionData Man page Source code
listGenomeFilters Man page Source code
listReadPairs Source code
listRearrangements2 Source code
list_region_levels Source code
list_tx_by_query Source code
loadOrgDb Source code
loadTx Man page Source code
loadTxDb Man page Source code
loadTxdbTranscripts Man page Source code
logicalList Source code
makeAGraph Man page Source code
makeAGraph2 Source code
makeGAlignmentPairs2 Source code
make_levels_unique Source code
mapTagsToCluster Source code
mapq Source code
maxClusterSize Man page
maxClusterSize,RearrangementParams-method Man page
maxRPsHomozygous Man page Source code
maxRatioObservedToExpected Man page Source code
max_proper_read_index Source code
maximumProportionInFilter Man page Source code
maximumWidth Man page Source code
mb_trans Source code
meltReadPairs Source code
meltReadPairs2 Source code
minClusterSize Man page
minClusterSize,RearrangementParams-method Man page
minFlankingHemizygous Man page Source code
minFlankingHomozygous Man page Source code
minGapWidth Man page
minGapWidth,RearrangementParams-method Man page
minNumberTagsPerCluster Man page
minNumberTagsPerCluster,RearrangementParams-method Man page
minRPsHemizygous Man page Source code
minSegmeanDiff Man page Source code
minimumBasepairCoverage Source code
minimumBinSize Source code
minimumGapWidth Man page Source code
minimumWidth Man page Source code
modalRearrangement Man page
modalRearrangement,Rearrangement,ANY-method Man page
modalRearrangement,Rearrangement-method Man page
modalRearrangement,RearrangementList-method Man page
modalRearrangement<- Man page
modalRearrangement<-,Rearrangement-method Man page
modelBackground Source code
modelGC2 Source code
multipleAlignmentRecords Source code
multipleAlignmentRecords2 Source code
myfilter Source code
name.left Man page
name.left,ExonSubset-method Man page
name.right Man page
name.right, Man page
name.right,ExonSubset-method Man page
names,ClippedTranscripts-class Man page
names,ClippedTranscripts-method Man page
names,ExonSubset-method Man page
names,Rearrangement-method Man page
names,RearrangementList-method Man page
names,StructuralVariant-method Man page
names<-,AmpliconGraph,ANY-method Man page
nearAmplicon Source code
nearDeletion Source code
noPrematureStop Man page Source code
node1 Source code Source code
node2 Source code Source code
nodes,AmpliconGraph-method Man page
nonAmpliconGranges,GRanges-method Man page
nonAmpliconRanges,AmpliconGraph-method Man page
nonampliconRanges Man page
nonampliconRanges,AmpliconGraph-method Man page
nonampliconRanges,GRanges-method Man page
not_in_filters Source code
numEdges,AmpliconGraph-method Man page
numNodes,AmpliconGraph-method Man page
number5pAminoAcids Source code
number5pAminoAcids_list Source code
numberAlignmentRecords Source code
numberAnchored Source code
numberFusions Man page
numberFusions,TranscriptsFusion-method Man page
numberImproper Man page Source code
numberLeftCodons Source code
numberLinkingRP Man page
numberLinkingRP,Rearrangement-method Man page
numberLinkingRP,RearrangementList-method Man page
numberOverlappingDeletions Man page Source code
numberSpanningAmplicons Source code
numberSplitReads Source code
object@id) Man page
orderEdgesByIndexOfOverlap Source code
organizeReads Man page Source code
organizeReferenceByFrame Man page Source code
outlierFrequencyPerBin Source code
outliers Source code
overlappingTranscripts Source code
overlapsAny,RearrangementList,GRanges-method Man page
overlapsAnyTranscript Source code
overlapsBlatRecord Source code
overlapsCNV Source code
overlapsGermline Source code
overlapsGermlineRear Source code
overlapsLinkedBins Source code
partitionAASequence Man page Source code
partitionAASequence_oneframe Source code
partitioning Man page
partitioning,Rearrangement-method Man page
paths Man page
paths,PreprocessViews2-method Man page
paths<- Man page
paths<-,PreprocessViews2-method Man page
pdata Man page
peelLegend Source code
percentLinking Man page Source code Source code
percentModalType Man page
percentModalType,RearrangementParams-method Man page
percentRearrangement Man page
percentRearrangement,Rearrangement,ANY-method Man page
percentRearrangement,Rearrangement-method Man page
percentRearrangement,RearrangementList-method Man page
percentRearrangement<- Man page
percentRearrangement<-,Rearrangement-method Man page
positionStopCodons Source code
preprocessData Man page Source code
preprocessData2 Source code
preprocessDirs Source code
promoterCDS Man page Source code
promoterTxName Source code
proper Man page
proper,StructuralVariant,GAlignmentPairs-method Man page
proper,StructuralVariant-method Man page
proper<- Man page
proper<-,StructuralVariant,GAlignmentPairs-method Man page
properAlignmentFlags Man page Source code
properAlignmentParams Man page Source code
properReadPairs Man page Source code
properReadPairs_bedops Man page Source code
properReadPairs_bedops2 Man page Source code
proteinFeatures Source code
proteinParams Source code
prp_makeRthinned Man page Source code
queryRanges Man page
queryRanges,AmpliconGraph,ANY-method Man page
queryRanges,AmpliconGraph-method Man page
queryRanges<- Man page
queryRanges<-,AmpliconGraph-method Man page
rFilters Man page Source code
ranges,AmpliconGraph,ANY-method Man page
ranges,AmpliconGraph-method Man page
ranges<-,AmpliconGraph-method Man page
rdsId Man page Source code
readBlat Man page Source code
readColors Source code
readOrientation Source code
readPairColors Source code
readPairs Man page
readPairs,StructuralVariant-method Man page
readPairsAsSegments Man page Source code
readPairsNearVariant Man page Source code
readPairsNearVariant_bedops Source code
readPairsNearVariant_bedops2 Source code
rearDataFrame Man page Source code
rearDataFrameList Man page Source code
rearStats Source code
rear_cds Man page
rear_cds-data Man page
rear_cgov7t Man page
rear_list Man page
rear_list-data Man page
rearrangedReadList Man page Source code
rearrangedReads Man page Source code
rearrangedReads2 Source code
rearrangementData Man page Source code
rearrangementTranscripts Source code
rearrangementTranscripts2 Source code
rearrangementType Man page Source code
rearrangement_list Man page
recurrentAmplicons Source code
recurrentDeletions Man page Source code
recurrentDrivers Man page Source code
reduceGenomeFilters Man page Source code
reduceProtein Source code
reduceTranscripts Source code
referenceDna3p Source code
referenceDna5p Source code
referenceProtein Man page Source code
reference_protein_3prime Source code
refineHomozygousBoundaryByHemizygousPlus Source code
removeAmbiguous Source code
removeAmbiguousAln Man page Source code
removeDuplicateIntervals Source code
removeDuplicateSv Source code
removeHemizygous Source code
removeOverlapsWithNullShortDesc Source code
removeReadsWithoutMate Source code
removeSameStateOverlapping Source code Source code
removeSameStateOverlapping2 Source code
remove_5prime_aminoAcids Source code
revise Source code
reviseDeletionBorders Source code
reviseEachJunction Source code
right Man page
right,ClippedTranscripts-method Man page
rightCodonIndices Source code
rightHemizygousHomolog Source code
rlist Man page
robustBackground Source code
rowRanges,PreprocessViews2,ANY-method Man page
rowRanges,PreprocessViews2-method Man page
rowRanges<-,PreprocessViews2,ANY-method Man page
rpSeparation Man page
rpSeparation,RearrangementParams-method Man page
rpSupportedDeletions Man page Source code
rpclustNames Source code
rpclustNamesMatrix Source code
sapply,RearrangementList-method Man page
sapply,StructuralVariant-method Man page
scale_x_kb Source code
scale_x_mb Man page Source code
segmentBins Man page Source code
segmentCoverage Source code
segmentExperiment Man page Source code
segmentInflections Source code
segments Man page
selectTx Source code
selfHits Source code
seqJunction Source code
seqJunctionNearTx Man page Source code
seqJunctionsInferredByPairedTags Source code
seqJunctionsInferredByPairedTags2 Man page Source code
seqJunctions_Rlist Man page Source code
seqinfo,PreprocessViews2-method Man page
seqinfo,StructuralVariant-method Man page
seqinfo<-,PreprocessViews2,seqinfo-method Man page
seqinfo<-,PreprocessViews2-method Man page
seqlengths,StructuralVariant-method Man page
seqlevels,PreprocessViews2-method Man page
seqlevels,RearrangementList-method Man page
seqsByRearrangement Source code
sequenceRanges Source code
sequenceRanges2 Source code
sequentialExonRanks Source code
setAmpliconGroups Source code
setAs Man page
setDrivers Source code
setGenes Source code
setScale,PreprocessViews2-method Man page
setScale<- Man page
setScale<-,PreprocessViews2-method Man page
singleAnchorHits Source code
sort,StructuralVariant-method Man page
sortByRead1 Man page Source code
splitReads Man page
splitReads,Rearrangement,GRanges-method Man page
splitReads,Rearrangement-method Man page
splitReads,RearrangementList,GRangesList-method Man page
splitReads,RearrangementList-method Man page
splitReads<- Man page
splitReads<-,Rearrangement,GRanges-method Man page
splitReads<-,RearrangementList,GRangesList-method Man page
splitreadIntersection Source code
splitreadSide Source code
standardizeGRangesMetadata Source code
startAmpliconBoundary Source code
stopPositions_oneframe Source code
subsetByOverlaps2 Source code
summarizeGeneFreq Source code
svAF Man page Source code
sv_amp_makeQuery Man page Source code
sv_amplicon_exp Man page Source code
sv_amplicons Man page Source code
sv_amplicons2 Man page Source code
sv_amplicons2_bedops Man page Source code
sv_amplicons2_bedops2 Man page Source code
sv_del_makeQuery Man page Source code
sv_deletions Man page Source code
sv_deletions_bedops Man page Source code
sv_deletions_bedops2 Man page Source code
tag_sequenceExperiment Man page Source code
tags Man page
tags,Rearrangement,ANY-method Man page
tags,Rearrangement-method Man page
tags<- Man page
tags<-,Rearrangement-method Man page
thinProperPairs Man page Source code
thinReadPairQuery Source code
thinReadPairs Man page Source code
threshold Man page Source code
totalWidth Man page Source code Source code
transformCounts Source code
translateCDS Man page Source code
trellis Man page
trellis-package Man page
trimRangesOverlappingCentromere Source code
tumorProtein Man page Source code
tumor_protein Source code
twoAnchorHits Source code
txA Man page
txA,Transcripts-method Man page
txA<- Man page
txA<-,Transcripts,ANY-method Man page
txA<-,Transcripts-method Man page
txB Man page
txB,Transcripts-method Man page
txB<- Man page
txB<-,Transcripts,ANY-method Man page
txB<-,Transcripts-method Man page
txC Man page
txC,Transcripts-method Man page
txC<- Man page
txC<-,Transcripts,ANY-method Man page
txC<-,Transcripts-method Man page
txD Man page
txD,Transcripts-method Man page
txD<- Man page
txD<-,Transcripts,ANY-method Man page
txD<-,Transcripts-method Man page
type,Rearrangement-method Man page
type,RearrangementList-method Man page
typeGAPairs Source code
typeRead Source code
type_each Source code
type_rearrangement Man page Source code
uncouple Man page Source code
undo.SD Man page
undo.SD,SegmentParam-method Man page
undo.splits Man page
undo.splits,SegmentParam-method Man page
uniprotFeatures Man page Source code
unmapped_read Man page Source code
unmapped_read2 Source code
unmapped_read_bedops Man page Source code
unpairThenReduce Source code
updateImproperIndex Source code
updateImproperIndex2 Source code
updateRangesMetadata Source code
use_negative_coords Source code
validFirstR1 Source code
validFusions Man page Source code
validLastR1 Source code
validPairForDeletion Source code
variant Man page
variant,StructuralVariant-method Man page
variant<- Man page
variant<-,StructuralVariant,ANY-method Man page
variant<-,StructuralVariant,GRanges-method Man page
waveFun Source code
whichGeneInUniprot Source code
widthNotSpannedByFilter Source code
writeToFasta Man page Source code
writeUnmappedToFasta Man page Source code
cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.

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