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 | 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 |