A C D E F G I K L M N O P Q R S U V W misc
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-method | SummarizedExperiment instances |
assays<- | SummarizedExperiment instances |
assays<--method | SummarizedExperiment instances |
c-method | GRanges objects |
c-method | GappedAlignments objects |
cigar | GappedAlignments 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: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 | GRanges objects |
coerce-method | GRangesList objects |
coerce-method | GappedAlignments objects |
coerce-method | Seqinfo objects |
colData | SummarizedExperiment instances |
colData-method | SummarizedExperiment instances |
colData<- | SummarizedExperiment instances |
colData<--method | SummarizedExperiment instances |
countGenomicOverlaps | Count Read Hits in Genomic Features |
countGenomicOverlaps-method | Count Read Hits in Genomic Features |
countOverlaps-method | GRanges, GRangesList and GappedAlignments Interval Overlaps |
coverage-method | GRanges, GRangesList and GappedAlignments coverage |
coverage-methods | GRanges, GRangesList and GappedAlignments coverage |
dim-method | SummarizedExperiment instances |
dimnames-method | SummarizedExperiment instances |
dimnames<--method | SummarizedExperiment instances |
disjoin-method | GRanges objects |
distance-method | GRanges objects |
duplicated-method | Ordering and comparing genomic ranges |
elementMetadata-method | GRanges objects |
elementMetadata-method | GRangesList objects |
elementMetadata-method | GappedAlignments objects |
elementMetadata<--method | GRanges objects |
elementMetadata<--method | GRangesList objects |
end-method | GRanges objects |
end-method | GRangesList objects |
end-method | GappedAlignments objects |
end<--method | GRanges objects |
end<--method | GRangesList objects |
exptData | SummarizedExperiment instances |
exptData-method | SummarizedExperiment instances |
exptData<- | SummarizedExperiment instances |
exptData<--method | SummarizedExperiment instances |
findOverlaps-method | GRanges, GRangesList and GappedAlignments Interval Overlaps |
findOverlaps-methods | GRanges, GRangesList and GappedAlignments Interval Overlaps |
flank-method | GRanges objects |
flank-method | GRangesList objects |
follow-method | GRanges objects |
GappedAlignments | GappedAlignments objects |
GappedAlignments-class | GappedAlignments objects |
gaps-method | GRanges objects |
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 | Ordering and comparing 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 | GappedAlignments objects |
GRangesList | GRangesList objects |
GRangesList-class | GRangesList objects |
grg | GappedAlignments objects |
grglist | GappedAlignments objects |
grglist-method | GappedAlignments objects |
intersect-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
IntersectionNotEmpty | Count reads that map to genomic features |
IntersectionStrict | Count reads that map to genomic features |
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 |
isCircularWithKnownLength | Accessing sequence information |
isCircularWithKnownLength-method | Seqinfo objects |
isCircularWithKnownLength-method | Accessing sequence information |
isDisjoint-method | GRanges objects |
isDisjoint-method | GRangesList objects |
keepSeqlevels | seqlevels utility functions |
keepSeqlevels-method | seqlevels utility functions |
length-method | GRanges objects |
length-method | GappedAlignments objects |
length-method | Seqinfo objects |
makeGRangesListFromFeatureFragments | GRangesList objects |
match-method | GRanges, GRangesList and GappedAlignments Interval Overlaps |
merge-method | Seqinfo objects |
names-method | GRanges objects |
names-method | GappedAlignments objects |
names-method | Seqinfo objects |
names<--method | GRanges objects |
names<--method | GappedAlignments objects |
names<--method | Seqinfo objects |
narrow-method | GappedAlignments objects |
ngap-method | GappedAlignments objects |
order-method | Ordering and comparing genomic ranges |
pgap-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
pintersect-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
precede-method | GRanges objects |
psetdiff-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
punion-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
qnarrow | GappedAlignments objects |
qnarrow-method | GappedAlignments objects |
queryLoc2refLoc | CIGAR utility functions |
queryLocs2refLocs | CIGAR utility functions |
qwidth | GappedAlignments objects |
qwidth-method | GappedAlignments objects |
range-method | GRanges objects |
range-method | GRangesList objects |
ranges-method | GRanges objects |
ranges-method | GRangesList objects |
ranges-method | GappedAlignments objects |
ranges<--method | GRanges objects |
ranges<--method | GRangesList objects |
rank-method | Ordering and comparing genomic ranges |
readGappedAlignments | GappedAlignments objects |
reduce-method | GRanges objects |
reduce-method | GRangesList objects |
renameSeqlevels | seqlevels utility functions |
renameSeqlevels-method | seqlevels utility functions |
resize-method | GRanges objects |
restrict-method | GRanges objects |
restrict-method | GRangesList objects |
rglist | GappedAlignments objects |
rglist-method | GappedAlignments objects |
rname | GappedAlignments objects |
rname-method | GappedAlignments objects |
rname<- | GappedAlignments objects |
rname<--method | GappedAlignments objects |
rowData | SummarizedExperiment instances |
rowData-method | SummarizedExperiment instances |
rowData<- | SummarizedExperiment instances |
rowData<--method | SummarizedExperiment instances |
Seqinfo | Seqinfo objects |
seqinfo | Accessing sequence information |
Seqinfo-class | Seqinfo objects |
seqinfo-method | GRanges objects |
seqinfo-method | GRangesList objects |
seqinfo-method | GappedAlignments objects |
seqinfo<- | Accessing sequence information |
seqinfo<--method | GRanges objects |
seqinfo<--method | GRangesList objects |
seqinfo<--method | GappedAlignments objects |
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 | GRanges objects |
seqnames-method | GRangesList objects |
seqnames-method | GappedAlignments objects |
seqnames-method | Seqinfo objects |
seqnames<- | Accessing sequence information |
seqnames<--method | GRanges objects |
seqnames<--method | GRangesList objects |
seqnames<--method | GappedAlignments objects |
seqnames<--method | Seqinfo objects |
seqselect-method | GRanges objects |
seqselect<--method | GRanges objects |
setdiff-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
setops-methods | Set operations on GRanges/GRangesList/GappedAlignments objects |
shift-method | GRanges objects |
shift-method | GRangesList objects |
show-method | GRanges objects |
show-method | GRangesList objects |
show-method | GappedAlignments objects |
show-method | Seqinfo objects |
show-method | SummarizedExperiment instances |
SimpleGenomicRangesList-class | GenomicRangesList objects |
sort-method | Ordering and comparing genomic ranges |
split-method | GRanges objects |
splitCigar | CIGAR utility functions |
start-method | GRanges objects |
start-method | GRangesList objects |
start-method | GappedAlignments objects |
start<--method | GRanges objects |
start<--method | GRangesList objects |
strand | Accessing strand information |
strand-method | GRanges objects |
strand-method | GRangesList objects |
strand-method | GappedAlignments objects |
strand-method | Accessing strand information |
strand-methods | Accessing strand information |
strand<- | Accessing strand information |
strand<--method | GRanges objects |
strand<--method | GRangesList objects |
strand<--method | GappedAlignments objects |
subsetByOverlaps-method | GRanges, GRangesList and GappedAlignments Interval Overlaps |
summarizeCigarTable | CIGAR utility functions |
SummarizedExperiment | SummarizedExperiment instances |
SummarizedExperiment-class | SummarizedExperiment instances |
SummarizedExperiment-method | SummarizedExperiment instances |
summarizeOverlaps | Count reads that map to genomic features |
summarizeOverlaps-method | Count reads that map to genomic features |
Union | Count reads that map to genomic features |
union-method | Set operations on GRanges/GRangesList/GappedAlignments objects |
unique-method | Ordering and comparing genomic ranges |
unlist-method | GRangesList objects |
updateObject-method | GRanges objects |
updateObject-method | GRangesList objects |
updateObject-method | GappedAlignments objects |
updateObject-method | Seqinfo objects |
validCigar | CIGAR utility functions |
width-method | GRanges objects |
width-method | GRangesList objects |
width-method | GappedAlignments objects |
width<--method | GRanges objects |
width<--method | GRangesList objects |
window-method | GRanges objects |
%in%-method | GRanges, GRangesList and GappedAlignments Interval Overlaps |
<-method | Ordering and comparing genomic ranges |
<=-method | Ordering and comparing genomic ranges |
==-method | Ordering and comparing genomic ranges |
>-method | Ordering and comparing genomic ranges |
>=-method | Ordering and comparing genomic ranges |
[-method | GRanges objects |
[-method | GRangesList objects |
[-method | GappedAlignments objects |
[-method | Seqinfo objects |
[-method | SummarizedExperiment instances |
[<--method | GRanges objects |
[<--method | GRangesList objects |
[<--method | SummarizedExperiment instances |
[[<--method | GRangesList objects |