A C D E F G I L M N P Q R S U V W misc
%in%-method | GRanges and GRangesList Interval Overlaps |
%in%-method | GappedAlignments objects |
as.data.frame-method | GRanges objects |
as.data.frame-method | GRangesList objects |
as.data.frame-method | GappedAlignments objects |
c-method | GRanges 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:GRanges | GRanges objects |
class:GRangesList | GRangesList objects |
coerce-method | GRanges objects |
coerce-method | GRangesList objects |
countOverlaps-method | GRanges and GRangesList Interval Overlaps |
countOverlaps-method | GappedAlignments objects |
coverage-method | GRanges objects |
coverage-method | GRangesList objects |
coverage-method | GappedAlignments objects |
disjoin-method | GRanges objects |
elementMetadata-method | GRanges objects |
elementMetadata-method | GRangesList 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 |
findOverlaps-method | GRanges and GRangesList Interval Overlaps |
findOverlaps-method | GappedAlignments objects |
flank-method | GRanges objects |
GappedAlignments | GappedAlignments objects |
GappedAlignments-class | GappedAlignments objects |
gaps-method | GRanges objects |
GRanges | GRanges objects |
GRanges-class | GRanges objects |
GRangesList | GRangesList objects |
GRangesList-class | GRangesList objects |
grg | GappedAlignments objects |
grg-method | GappedAlignments objects |
grglist | GappedAlignments objects |
grglist-method | GappedAlignments objects |
intersect-method | GRanges and GRangesList Set and Parallel Set Operations |
length-method | GRanges objects |
length-method | GappedAlignments objects |
match-method | GRanges and GRangesList Interval Overlaps |
match-method | GappedAlignments objects |
names-method | GRanges objects |
names<--method | GRanges objects |
narrow-method | GappedAlignments objects |
pintersect-method | GRanges and GRangesList Set and Parallel Set Operations |
pintersect-method | GappedAlignments objects |
psetdiff-method | GRanges and GRangesList Set and Parallel Set Operations |
punion-method | GRanges and GRangesList Set and Parallel Set Operations |
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 |
ranges-method | GRanges objects |
ranges-method | GRangesList objects |
ranges<--method | GRanges objects |
ranges<--method | GRangesList objects |
readGappedAlignments | GappedAlignments objects |
reduce-method | GRanges objects |
resize-method | GRanges objects |
rev-method | GRanges objects |
rglist | GappedAlignments objects |
rglist-method | GappedAlignments objects |
rname | GappedAlignments objects |
rname-method | GappedAlignments objects |
rname<- | GappedAlignments objects |
rname<--method | GappedAlignments objects |
seqlengths | Accessing the sequence names and lengths stored in an object |
seqlengths-method | GRanges objects |
seqlengths-method | GRangesList objects |
seqlengths-method | GappedAlignments objects |
seqlengths<- | Accessing the sequence names and lengths stored in an object |
seqlengths<--method | GRanges objects |
seqlengths<--method | GRangesList objects |
seqlengths<--method | GappedAlignments objects |
seqnames | Accessing the sequence names and lengths stored in an object |
seqnames-method | GRanges objects |
seqnames-method | GRangesList objects |
seqnames-method | GappedAlignments objects |
seqnames<- | Accessing the sequence names and lengths stored in an object |
seqnames<--method | GRanges objects |
seqnames<--method | GRangesList objects |
seqnames<--method | GappedAlignments objects |
seqselect-method | GRanges objects |
seqselect<--method | GRanges objects |
setdiff-method | GRanges and GRangesList Set and Parallel Set Operations |
shift-method | GRanges objects |
shift-method | GRangesList objects |
show-method | GRanges objects |
show-method | GRangesList objects |
show-method | GappedAlignments objects |
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 |
subsetByOverlaps-method | GRanges and GRangesList Interval Overlaps |
subsetByOverlaps-method | GappedAlignments objects |
summarizeCigarTable | CIGAR utility functions |
union-method | GRanges and GRangesList Set and Parallel Set Operations |
unlist-method | GRangesList 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 |
[-method | GRanges objects |
[-method | GRangesList objects |
[-method | GappedAlignments objects |
[<--method | GRanges objects |
[<--method | GRangesList objects |