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A C D E F G I K L M N O P Q R S T U V W misc
| as.data.frame-method | GAlignmentsList objects |
| as.data.frame-method | GRanges objects |
| as.data.frame-method | GRangesList objects |
| as.data.frame-method | GappedAlignments objects |
| as.data.frame-method | Seqinfo objects |
| assay | SummarizedExperiment instances |
| assay-method | SummarizedExperiment instances |
| assay<- | SummarizedExperiment instances |
| assay<--method | SummarizedExperiment instances |
| assays | SummarizedExperiment instances |
| Assays-class | SummarizedExperiment instances |
| assays-method | SummarizedExperiment instances |
| assays<- | SummarizedExperiment instances |
| assays<--method | SummarizedExperiment instances |
| c-method | GAlignmentsList objects |
| c-method | GRanges objects |
| c-method | GappedAlignmentPairs objects |
| c-method | GappedAlignments objects |
| cbind-method | SummarizedExperiment instances |
| checkConstraint | Enforcing constraints thru Constraint objects |
| cigar | GappedAlignments objects |
| cigar-method | GAlignmentsList objects |
| cigar-method | GappedAlignments objects |
| cigar-utils | CIGAR utility functions |
| cigarNarrow | CIGAR utility functions |
| cigarOpTable | CIGAR utility functions |
| cigarQNarrow | CIGAR utility functions |
| cigarToCigarTable | CIGAR utility functions |
| cigarToIRanges | CIGAR utility functions |
| cigarToIRangesListByAlignment | CIGAR utility functions |
| cigarToIRangesListByRName | CIGAR utility functions |
| cigarToQWidth | CIGAR utility functions |
| cigarToRleList | CIGAR utility functions |
| cigarToWidth | CIGAR utility functions |
| class:Constraint | Enforcing constraints thru Constraint objects |
| class:ConstraintORNULL | Enforcing constraints thru Constraint objects |
| class:GAlignmentsList | GAlignmentsList objects |
| class:GappedAlignmentPairs | GappedAlignmentPairs objects |
| class:GappedAlignments | GappedAlignments objects |
| class:GenomicRanges | GRanges objects |
| class:GenomicRangesList | GenomicRangesList objects |
| class:GRanges | GRanges objects |
| class:GRangesList | GRangesList objects |
| class:Seqinfo | Seqinfo objects |
| class:SimpleGenomicRangesList | GenomicRangesList objects |
| coerce-method | GAlignmentsList objects |
| coerce-method | GRanges objects |
| coerce-method | GRangesList objects |
| coerce-method | GappedAlignmentPairs objects |
| coerce-method | GappedAlignments objects |
| coerce-method | GenomicRangesList objects |
| coerce-method | Seqinfo objects |
| coerce-method | Mapping ranges between sequences |
| colData | SummarizedExperiment instances |
| colData-method | SummarizedExperiment instances |
| colData<- | SummarizedExperiment instances |
| colData<--method | SummarizedExperiment instances |
| compare-method | Comparing and ordering genomic ranges |
| compare-method | SummarizedExperiment instances |
| Constraint | Enforcing constraints thru Constraint objects |
| constraint | Enforcing constraints thru Constraint objects |
| Constraint-class | Enforcing constraints thru Constraint objects |
| constraint<- | Enforcing constraints thru Constraint objects |
| ConstraintORNULL | Enforcing constraints thru Constraint objects |
| ConstraintORNULL-class | Enforcing constraints thru Constraint objects |
| Constraints | Enforcing constraints thru Constraint objects |
| countCompatibleOverlaps | encodeOverlaps method for GRangesList objects, and related utilities |
| countMatches-method | Comparing and ordering genomic ranges |
| countMatches-method | Finding overlapping genomic ranges |
| countOverlaps-method | SummarizedExperiment instances |
| countOverlaps-method | Finding overlapping genomic ranges |
| coverage-method | SummarizedExperiment instances |
| coverage-method | Coverage of a GRanges, GRangesList, GappedAlignments, or GappedAlignmentPairs object |
| coverage-methods | Coverage of a GRanges, GRangesList, GappedAlignments, or GappedAlignmentPairs object |
| dim-method | SummarizedExperiment instances |
| dimnames-method | SummarizedExperiment instances |
| dimnames<--method | SummarizedExperiment instances |
| disjoin-method | GRangesList objects |
| disjoin-method | Inter range transformations of a GenomicRanges object |
| disjointBins-method | SummarizedExperiment instances |
| disjointBins-method | Inter range transformations of a GenomicRanges object |
| distance-method | SummarizedExperiment instances |
| distance-method | Finding the nearest genomic range neighbor |
| distanceToNearest-method | SummarizedExperiment instances |
| distanceToNearest-method | Finding the nearest genomic range neighbor |
| duplicated-method | Comparing and ordering genomic ranges |
| duplicated-method | SummarizedExperiment instances |
| duplicated.GenomicRanges | Comparing and ordering genomic ranges |
| elementMetadata-method | GAlignmentsList objects |
| elementMetadata-method | GRangesList objects |
| elementMetadata-method | SummarizedExperiment instances |
| elementMetadata<--method | GAlignmentsList objects |
| elementMetadata<--method | GRanges objects |
| elementMetadata<--method | GRangesList objects |
| elementMetadata<--method | GappedAlignmentPairs objects |
| elementMetadata<--method | GappedAlignments objects |
| elementMetadata<--method | SummarizedExperiment instances |
| encodeOverlaps-method | encodeOverlaps method for GRangesList objects, and related utilities |
| encodeOverlaps-methods | encodeOverlaps method for GRangesList objects, and related utilities |
| end-method | GAlignmentsList objects |
| end-method | GRanges objects |
| end-method | GRangesList objects |
| end-method | GappedAlignments objects |
| end-method | SummarizedExperiment instances |
| end<--method | GRanges objects |
| end<--method | GRangesList objects |
| end<--method | SummarizedExperiment instances |
| exptData | SummarizedExperiment instances |
| exptData-method | SummarizedExperiment instances |
| exptData<- | SummarizedExperiment instances |
| exptData<--method | SummarizedExperiment instances |
| extractQueryStartInTranscript | encodeOverlaps method for GRangesList objects, and related utilities |
| extractSkippedExonRanks | encodeOverlaps method for GRangesList objects, and related utilities |
| extractSkippedExonRanks-method | encodeOverlaps method for GRangesList objects, and related utilities |
| extractSpannedExonRanks | encodeOverlaps method for GRangesList objects, and related utilities |
| extractSpannedExonRanks-method | encodeOverlaps method for GRangesList objects, and related utilities |
| extractSteppedExonRanks | encodeOverlaps method for GRangesList objects, and related utilities |
| extractSteppedExonRanks-method | encodeOverlaps method for GRangesList objects, and related utilities |
| findCompatibleOverlaps | encodeOverlaps method for GRangesList objects, and related utilities |
| findCompatibleOverlaps-method | encodeOverlaps method for GRangesList objects, and related utilities |
| findMatches-method | Comparing and ordering genomic ranges |
| findMatches-method | Finding overlapping genomic ranges |
| findOverlaps-method | SummarizedExperiment instances |
| findOverlaps-method | Finding overlapping genomic ranges |
| findOverlaps-methods | Finding overlapping genomic ranges |
| findSpliceOverlaps | Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events |
| findSpliceOverlaps-method | Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events |
| findSpliceOverlaps-methods | Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events |
| first | GappedAlignmentPairs objects |
| first-method | GappedAlignmentPairs objects |
| flank-method | GRangesList objects |
| flank-method | SummarizedExperiment instances |
| flank-method | Intra range transformations of a GenomicRanges object |
| flipQuery | encodeOverlaps method for GRangesList objects, and related utilities |
| follow-method | SummarizedExperiment instances |
| follow-method | Finding the nearest genomic range neighbor |
| GAlignmentsList | GAlignmentsList objects |
| GAlignmentsList-class | GAlignmentsList objects |
| GappedAlignmentPairs | GappedAlignmentPairs objects |
| GappedAlignmentPairs-class | GappedAlignmentPairs objects |
| GappedAlignments | GappedAlignments objects |
| GappedAlignments-class | GappedAlignments objects |
| gaps-method | Inter range transformations of a GenomicRanges object |
| genome | Accessing sequence information |
| genome-method | Seqinfo objects |
| genome-method | Accessing sequence information |
| genome<- | Accessing sequence information |
| genome<--method | Seqinfo objects |
| genome<--method | Accessing sequence information |
| GenomicRanges | GRanges objects |
| GenomicRanges-class | GRanges objects |
| GenomicRanges-comparison | Comparing and ordering genomic ranges |
| GenomicRangesList | GenomicRangesList objects |
| GenomicRangesList-class | GenomicRangesList objects |
| GenomicRangesORGRangesList-class | GRanges objects |
| GenomicRangesORmissing-class | GRanges objects |
| GRanges | GRanges objects |
| granges | GappedAlignments objects |
| GRanges-class | GRanges objects |
| granges-method | GAlignmentsList objects |
| granges-method | GappedAlignmentPairs objects |
| granges-method | GappedAlignments objects |
| granges-method | SummarizedExperiment instances |
| granges-method | Mapping ranges between sequences |
| GRangesList | GRangesList objects |
| GRangesList-class | GRangesList objects |
| grglist | GappedAlignments objects |
| grglist-method | GAlignmentsList objects |
| grglist-method | GappedAlignmentPairs objects |
| grglist-method | GappedAlignments objects |
| inter-range-methods | Inter range transformations of a GenomicRanges object |
| intersect-method | Seqinfo objects |
| intersect-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
| IntersectionNotEmpty | Perform overlap queries between reads and genomic features |
| IntersectionStrict | Perform overlap queries between reads and genomic features |
| intra-range-methods | Intra range transformations of a GenomicRanges object |
| introns | GappedAlignments objects |
| introns-method | GAlignmentsList objects |
| introns-method | GappedAlignmentPairs objects |
| introns-method | GappedAlignments objects |
| isCircular | Accessing sequence information |
| isCircular-method | Seqinfo objects |
| isCircular-method | Accessing sequence information |
| isCircular<- | Accessing sequence information |
| isCircular<--method | Seqinfo objects |
| isCircular<--method | Accessing sequence information |
| isCompatibleWithSkippedExons | encodeOverlaps method for GRangesList objects, and related utilities |
| isCompatibleWithSkippedExons-method | encodeOverlaps method for GRangesList objects, and related utilities |
| isCompatibleWithSplicing | encodeOverlaps method for GRangesList objects, and related utilities |
| isCompatibleWithSplicing-method | encodeOverlaps method for GRangesList objects, and related utilities |
| isDisjoint-method | GRangesList objects |
| isDisjoint-method | SummarizedExperiment instances |
| isDisjoint-method | Inter range transformations of a GenomicRanges object |
| isProperPair | GappedAlignmentPairs objects |
| isProperPair-method | GappedAlignmentPairs objects |
| keepSeqlevels | seqlevels utility functions |
| keepSeqlevels-method | seqlevels utility functions |
| last | GappedAlignmentPairs objects |
| last-method | GappedAlignmentPairs objects |
| left | GappedAlignmentPairs objects |
| left-method | GappedAlignmentPairs objects |
| length-method | GRanges objects |
| length-method | GappedAlignmentPairs objects |
| length-method | GappedAlignments objects |
| length-method | Seqinfo objects |
| makeGAlignmentsListFromFeatureFragments | GAlignmentsList objects |
| makeGRangesListFromFeatureFragments | GRangesList objects |
| makeSeqnameIds | Assigns a unique ID to each unique sequence name |
| map-method | Mapping ranges between sequences |
| match-method | Comparing and ordering genomic ranges |
| match-method | SummarizedExperiment instances |
| match-method | Finding overlapping genomic ranges |
| mcols-method | SummarizedExperiment instances |
| mcols<--method | SummarizedExperiment instances |
| merge-method | Seqinfo objects |
| names-method | GAlignmentsList objects |
| names-method | GRanges objects |
| names-method | GappedAlignmentPairs objects |
| names-method | GappedAlignments objects |
| names-method | Seqinfo objects |
| names<--method | GAlignmentsList objects |
| names<--method | GRanges objects |
| names<--method | GappedAlignmentPairs objects |
| names<--method | GappedAlignments objects |
| names<--method | Seqinfo objects |
| narrow-method | SummarizedExperiment instances |
| narrow-method | Intra range transformations of a GenomicRanges object |
| nearest-method | SummarizedExperiment instances |
| nearest-method | Finding the nearest genomic range neighbor |
| nearest-methods | Finding the nearest genomic range neighbor |
| ngap-method | GAlignmentsList objects |
| ngap-method | GappedAlignmentPairs objects |
| ngap-method | GappedAlignments objects |
| Ops-method | Intra range transformations of a GenomicRanges object |
| order-method | Comparing and ordering genomic ranges |
| order-method | SummarizedExperiment instances |
| overlapsAny-method | SummarizedExperiment instances |
| overlapsAny-method | Finding overlapping genomic ranges |
| pgap-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
| phicoef | Calculate the "phi coefficient" between two binary variables |
| pintersect-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
| precede-method | SummarizedExperiment instances |
| precede-method | Finding the nearest genomic range neighbor |
| promoters-method | GRangesList objects |
| promoters-method | Intra range transformations of a GenomicRanges object |
| psetdiff-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
| punion-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
| qnarrow | GappedAlignments objects |
| qnarrow-method | GAlignmentsList objects |
| qnarrow-method | GappedAlignments objects |
| queryLoc2refLoc | CIGAR utility functions |
| queryLocs2refLocs | CIGAR utility functions |
| qwidth | GappedAlignments objects |
| qwidth-method | GAlignmentsList objects |
| qwidth-method | GappedAlignments objects |
| range-method | GRangesList objects |
| range-method | Inter range transformations of a GenomicRanges object |
| ranges-method | GAlignmentsList objects |
| ranges-method | GRanges objects |
| ranges-method | GRangesList objects |
| ranges-method | GappedAlignments objects |
| ranges-method | SummarizedExperiment instances |
| ranges<--method | GRanges objects |
| ranges<--method | GRangesList objects |
| ranges<--method | SummarizedExperiment instances |
| rank-method | Comparing and ordering genomic ranges |
| rank-method | SummarizedExperiment instances |
| rbind-method | SummarizedExperiment instances |
| readGAlignmentsList | GAlignmentsList objects |
| readGappedAlignmentPairs | GappedAlignmentPairs objects |
| readGappedAlignments | GappedAlignments objects |
| reduce-method | GRangesList objects |
| reduce-method | Inter range transformations of a GenomicRanges object |
| renameSeqlevels | seqlevels utility functions |
| renameSeqlevels-method | seqlevels utility functions |
| resize-method | SummarizedExperiment instances |
| resize-method | Intra range transformations of a GenomicRanges object |
| restrict-method | GRangesList objects |
| restrict-method | SummarizedExperiment instances |
| restrict-method | Intra range transformations of a GenomicRanges object |
| rglist | GappedAlignments objects |
| rglist-method | GAlignmentsList objects |
| rglist-method | GappedAlignments objects |
| right | GappedAlignmentPairs objects |
| right-method | GappedAlignmentPairs objects |
| rname | GappedAlignments objects |
| rname-method | GAlignmentsList objects |
| rname-method | GappedAlignments objects |
| rname<- | GappedAlignments objects |
| rname<--method | GAlignmentsList objects |
| rname<--method | GappedAlignments objects |
| rowData | SummarizedExperiment instances |
| rowData-method | SummarizedExperiment instances |
| rowData<- | SummarizedExperiment instances |
| rowData<--method | SummarizedExperiment instances |
| score-method | GRanges objects |
| score-method | GRangesList objects |
| selectEncodingWithCompatibleStrand | encodeOverlaps method for GRangesList objects, and related utilities |
| Seqinfo | Seqinfo objects |
| seqinfo | Accessing sequence information |
| Seqinfo-class | Seqinfo objects |
| seqinfo-method | GAlignmentsList objects |
| seqinfo-method | GRanges objects |
| seqinfo-method | GRangesList objects |
| seqinfo-method | GappedAlignmentPairs objects |
| seqinfo-method | GappedAlignments objects |
| seqinfo-method | SummarizedExperiment instances |
| seqinfo-method | Accessing sequence information |
| seqinfo<- | Accessing sequence information |
| seqinfo<--method | GAlignmentsList objects |
| seqinfo<--method | GRanges objects |
| seqinfo<--method | GRangesList objects |
| seqinfo<--method | GappedAlignmentPairs objects |
| seqinfo<--method | GappedAlignments objects |
| seqinfo<--method | SummarizedExperiment instances |
| seqinfo<--method | Accessing sequence information |
| seqlengths | Accessing sequence information |
| seqlengths-method | Seqinfo objects |
| seqlengths-method | Accessing sequence information |
| seqlengths<- | Accessing sequence information |
| seqlengths<--method | Seqinfo objects |
| seqlengths<--method | Accessing sequence information |
| seqlevels | Accessing sequence information |
| seqlevels-method | Seqinfo objects |
| seqlevels-method | Accessing sequence information |
| seqlevels<- | Accessing sequence information |
| seqlevels<--method | Seqinfo objects |
| seqlevels<--method | Accessing sequence information |
| seqnames | Accessing sequence information |
| seqnames-method | GAlignmentsList objects |
| seqnames-method | GRanges objects |
| seqnames-method | GRangesList objects |
| seqnames-method | GappedAlignmentPairs objects |
| seqnames-method | GappedAlignments objects |
| seqnames-method | Seqinfo objects |
| seqnames-method | SummarizedExperiment instances |
| seqnames-method | Accessing sequence information |
| seqnames<- | Accessing sequence information |
| seqnames<--method | GAlignmentsList objects |
| seqnames<--method | GRanges objects |
| seqnames<--method | GRangesList objects |
| seqnames<--method | GappedAlignments objects |
| seqnames<--method | Seqinfo objects |
| seqnameStyle | Accessing sequence information |
| seqnameStyle-method | Seqinfo objects |
| seqnameStyle-method | Accessing sequence information |
| seqnameStyle<- | Accessing sequence information |
| seqnameStyle<--method | Seqinfo objects |
| seqnameStyle<--method | Accessing sequence information |
| seqselect-method | GRanges objects |
| seqselect-method | SummarizedExperiment instances |
| seqselect<--method | GRanges objects |
| seqselect<--method | SummarizedExperiment instances |
| setdiff-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
| setops-methods | Set operations on GRanges/GRangesList/GappedAlignments objects |
| shift-method | GRangesList objects |
| shift-method | SummarizedExperiment instances |
| shift-method | Intra range transformations of a GenomicRanges object |
| show-method | GAlignmentsList objects |
| show-method | GRanges objects |
| show-method | GRangesList objects |
| show-method | GappedAlignmentPairs objects |
| show-method | GappedAlignments objects |
| show-method | Seqinfo objects |
| show-method | SummarizedExperiment instances |
| SimpleGenomicRangesList-class | GenomicRangesList objects |
| sort-method | SummarizedExperiment instances |
| split-method | SummarizedExperiment instances |
| splitAsListReturnedClass,GRange | GRanges objects |
| splitAsListReturnedClass-method | GRanges objects |
| splitAsListReturnedClass-method | GappedAlignments objects |
| splitAsListReturnedClass-method | SummarizedExperiment instances |
| splitCigar | CIGAR utility functions |
| start-method | GAlignmentsList objects |
| start-method | GRanges objects |
| start-method | GRangesList objects |
| start-method | GappedAlignments objects |
| start-method | SummarizedExperiment instances |
| start<--method | GRanges objects |
| start<--method | GRangesList objects |
| start<--method | SummarizedExperiment instances |
| strand-method | GAlignmentsList objects |
| strand-method | GRanges objects |
| strand-method | GRangesList objects |
| strand-method | GappedAlignmentPairs objects |
| strand-method | GappedAlignments objects |
| strand-method | SummarizedExperiment instances |
| strand-method | Strand utilities |
| strand-utils | Strand utilities |
| strand<--method | GAlignmentsList objects |
| strand<--method | GRanges objects |
| strand<--method | GRangesList objects |
| strand<--method | GappedAlignmentPairs objects |
| strand<--method | GappedAlignments objects |
| strand<--method | SummarizedExperiment instances |
| strand<--method | Strand utilities |
| subsetByOverlaps-method | SummarizedExperiment instances |
| subsetByOverlaps-method | Finding overlapping genomic ranges |
| summarizeCigarTable | CIGAR utility functions |
| SummarizedExperiment | SummarizedExperiment instances |
| SummarizedExperiment-class | SummarizedExperiment instances |
| SummarizedExperiment-method | SummarizedExperiment instances |
| summarizeOverlaps | Perform overlap queries between reads and genomic features |
| summarizeOverlaps-method | Perform overlap queries between reads and genomic features |
| trim-method | Intra range transformations of a GenomicRanges object |
| Union | Perform overlap queries between reads and genomic features |
| union-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
| unlist-method | GappedAlignmentPairs objects |
| updateObject-method | GAlignmentsList objects |
| updateObject-method | GRanges objects |
| updateObject-method | GRangesList objects |
| updateObject-method | GappedAlignments objects |
| updateObject-method | Seqinfo objects |
| updateObject-method | SummarizedExperiment instances |
| validCigar | CIGAR utility functions |
| values-method | SummarizedExperiment instances |
| values<--method | SummarizedExperiment instances |
| width-method | GAlignmentsList objects |
| width-method | GRanges objects |
| width-method | GRangesList objects |
| width-method | GappedAlignments objects |
| width-method | SummarizedExperiment instances |
| width<--method | GRanges objects |
| width<--method | GRangesList objects |
| width<--method | SummarizedExperiment instances |
| window-method | GRanges objects |
| $-method | GRanges objects |
| $-method | SummarizedExperiment instances |
| $<--method | GRanges objects |
| $<--method | SummarizedExperiment instances |
| %in%-method | Comparing and ordering genomic ranges |
| %in%-method | SummarizedExperiment instances |
| %in%-method | Finding overlapping genomic ranges |
| <=-method | Comparing and ordering genomic ranges |
| ==-method | Comparing and ordering genomic ranges |
| [-method | GAlignmentsList objects |
| [-method | GRanges objects |
| [-method | GRangesList objects |
| [-method | GappedAlignmentPairs objects |
| [-method | GappedAlignments objects |
| [-method | Seqinfo objects |
| [-method | SummarizedExperiment instances |
| [<--method | GAlignmentsList objects |
| [<--method | GRanges objects |
| [<--method | GRangesList objects |
| [<--method | SummarizedExperiment instances |
| [[-method | GappedAlignmentPairs objects |
| [[-method | SummarizedExperiment instances |
| [[<--method | GAlignmentsList objects |
| [[<--method | GRangesList objects |
| [[<--method | SummarizedExperiment instances |