A B C D E F G I L M N O P R S T U V W misc
absoluteRanges | Transform genomic ranges into "absolute" ranges |
as.character-method | GRanges objects |
as.data.frame-method | GRanges objects |
as.factor-method | GRanges objects |
assay | SummarizedExperiment instances |
assay-method | SummarizedExperiment instances |
assay<- | SummarizedExperiment instances |
assay<--method | SummarizedExperiment instances |
assayNames | SummarizedExperiment instances |
assayNames-method | SummarizedExperiment instances |
assayNames<- | SummarizedExperiment instances |
assayNames<--method | SummarizedExperiment instances |
assays | SummarizedExperiment instances |
Assays-class | SummarizedExperiment instances |
assays-method | SummarizedExperiment instances |
assays<- | SummarizedExperiment instances |
assays<--method | SummarizedExperiment instances |
bindAsGRanges | Manipulating genomic variables |
binnedAverage | Manipulating genomic variables |
c-method | GRanges objects |
cbind-method | SummarizedExperiment instances |
checkConstraint | Enforcing constraints thru Constraint objects |
class:Constraint | Enforcing constraints thru Constraint objects |
class:ConstraintORNULL | Enforcing constraints thru Constraint objects |
class:DelegatingGenomicRanges | DelegatingGenomicRanges objects |
class:GenomicRanges | GRanges objects |
class:GenomicRangesList | GenomicRangesList objects |
class:GIntervalTree | GIntervalTree objects |
class:GNCList | GNCList objects |
class:GRanges | GRanges objects |
class:GRangesList | GRangesList objects |
class:SimpleGenomicRangesList | GenomicRangesList objects |
coerce-method | GIntervalTree objects |
coerce-method | GNCList objects |
coerce-method | GRanges objects |
coerce-method | GRangesList objects |
coerce-method | GenomicRangesList objects |
coerce-method | SummarizedExperiment instances |
coerce-method | Manipulating genomic variables |
coerce-method | Make a GRanges object from a data.frame or DataFrame |
colData | SummarizedExperiment instances |
colData-method | SummarizedExperiment instances |
colData<- | SummarizedExperiment instances |
colData<--method | SummarizedExperiment instances |
compare | Comparing and ordering genomic ranges |
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 |
countOverlaps | Finding overlapping genomic ranges |
countOverlaps-method | SummarizedExperiment instances |
countOverlaps-method | Finding overlapping genomic ranges |
coverage | Coverage of a GRanges or GRangesList object |
coverage-method | SummarizedExperiment instances |
coverage-method | Coverage of a GRanges or GRangesList object |
coverage-methods | Coverage of a GRanges or GRangesList object |
DelegatingGenomicRanges-class | DelegatingGenomicRanges objects |
dim-method | SummarizedExperiment instances |
dimnames-method | SummarizedExperiment instances |
dimnames<--method | SummarizedExperiment instances |
disjoin | Inter range transformations of a GenomicRanges or GRangesList object |
disjoin-method | Inter range transformations of a GenomicRanges or GRangesList object |
disjointBins | Inter range transformations of a GenomicRanges or GRangesList object |
disjointBins-method | SummarizedExperiment instances |
disjointBins-method | Inter range transformations of a GenomicRanges or GRangesList object |
distance | Finding the nearest genomic range neighbor |
distance-method | SummarizedExperiment instances |
distance-method | Finding the nearest genomic range neighbor |
distanceToNearest | 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 | GIntervalTree objects |
elementMetadata-method | GRangesList objects |
elementMetadata-method | SummarizedExperiment instances |
elementMetadata<--method | GRangesList objects |
elementMetadata<--method | SummarizedExperiment instances |
end-method | GIntervalTree objects |
end-method | GNCList objects |
end-method | GRanges objects |
end-method | GRangesList 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 |
findOverlaps | Finding overlapping genomic ranges |
findOverlaps-method | SummarizedExperiment instances |
findOverlaps-method | Finding overlapping genomic ranges |
findOverlaps-methods | Finding overlapping genomic ranges |
flank | Intra range transformations of a GRanges or GRangesList object |
flank-method | SummarizedExperiment instances |
flank-method | Intra range transformations of a GRanges or GRangesList object |
follow | Finding the nearest genomic range neighbor |
follow-method | SummarizedExperiment instances |
follow-method | Finding the nearest genomic range neighbor |
gaps | Inter range transformations of a GenomicRanges or GRangesList object |
gaps-method | Inter range transformations of a GenomicRanges or GRangesList object |
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 |
genomicvariables | Manipulating genomic variables |
genomicvars | Manipulating genomic variables |
GIntervalTree | GIntervalTree objects |
GIntervalTree-class | GIntervalTree objects |
GNCList | GNCList objects |
GNCList-class | GNCList objects |
GRanges | GRanges objects |
granges | Squeeze the ranges out of a range-based object |
GRanges-class | GRanges objects |
granges-method | GNCList objects |
granges-method | GRanges objects |
granges-method | SummarizedExperiment instances |
GRangesList | GRangesList objects |
GRangesList-class | GRangesList objects |
grglist | Squeeze the ranges out of a range-based object |
inter-range-methods | Inter range transformations of a GenomicRanges or GRangesList object |
intersect-method | Set operations on GRanges and GRangesList objects |
intra-range-methods | Intra range transformations of a GRanges or GRangesList object |
is.unsorted-method | Comparing and ordering genomic ranges |
isDisjoint | Inter range transformations of a GenomicRanges or GRangesList object |
isDisjoint-method | SummarizedExperiment instances |
isDisjoint-method | Inter range transformations of a GenomicRanges or GRangesList object |
isSmallGenome | Transform genomic ranges into "absolute" ranges |
length-method | GNCList objects |
length-method | GRanges objects |
makeGRangesFromDataFrame | Make a GRanges object from a data.frame or DataFrame |
makeGRangesListFromFeatureFragments | GRangesList objects |
makeSummarizedExperimentFromExpressionSet | Make a SummarizedExperiment object from an ExpressionSet |
mapCoords | Mapping ranges between sequences |
mapCoords-method | Mapping ranges between sequences |
mapCoords-methods | Mapping ranges between sequences |
match-method | Comparing and ordering genomic ranges |
mcolAsRleList | Manipulating genomic variables |
mcols-method | SummarizedExperiment instances |
mcols<--method | SummarizedExperiment instances |
names-method | GIntervalTree objects |
names-method | GNCList objects |
names-method | GRanges objects |
names<--method | GRanges objects |
narrow | Intra range transformations of a GRanges or GRangesList object |
narrow-method | SummarizedExperiment instances |
narrow-method | Intra range transformations of a GRanges or GRangesList object |
nearest | Finding the nearest genomic range neighbor |
nearest-method | SummarizedExperiment instances |
nearest-method | Finding the nearest genomic range neighbor |
nearest-methods | Finding the nearest genomic range neighbor |
Ops-method | Intra range transformations of a GRanges or GRangesList object |
order-method | Comparing and ordering genomic ranges |
order-method | SummarizedExperiment instances |
overlapsAny | Finding overlapping genomic ranges |
overlapsAny-method | SummarizedExperiment instances |
overlapsAny-method | Finding overlapping genomic ranges |
pgap | Set operations on GRanges and GRangesList objects |
pgap-method | Set operations on GRanges and GRangesList objects |
phicoef | Calculate the "phi coefficient" between two binary variables |
pintersect | Set operations on GRanges and GRangesList objects |
pintersect-method | Set operations on GRanges and GRangesList objects |
pmapCoords | Mapping ranges between sequences |
pmapCoords-method | Mapping ranges between sequences |
precede | Finding the nearest genomic range neighbor |
precede-method | SummarizedExperiment instances |
precede-method | Finding the nearest genomic range neighbor |
promoters | Intra range transformations of a GRanges or GRangesList object |
promoters-method | Intra range transformations of a GRanges or GRangesList object |
psetdiff | Set operations on GRanges and GRangesList objects |
psetdiff-method | Set operations on GRanges and GRangesList objects |
punion | Set operations on GRanges and GRangesList objects |
punion-method | Set operations on GRanges and GRangesList objects |
range | Inter range transformations of a GenomicRanges or GRangesList object |
range-method | Inter range transformations of a GenomicRanges or GRangesList object |
range-squeezers | Squeeze the ranges out of a range-based object |
ranges-method | DelegatingGenomicRanges objects |
ranges-method | GIntervalTree objects |
ranges-method | GNCList objects |
ranges-method | GRanges objects |
ranges-method | GRangesList 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 |
reduce | Inter range transformations of a GenomicRanges or GRangesList object |
reduce-method | Inter range transformations of a GenomicRanges or GRangesList object |
relativeRanges | Transform genomic ranges into "absolute" ranges |
relistToClass-method | GRangesList objects |
resize | Intra range transformations of a GRanges or GRangesList object |
resize-method | SummarizedExperiment instances |
resize-method | Intra range transformations of a GRanges or GRangesList object |
restrict | Intra range transformations of a GRanges or GRangesList object |
restrict-method | SummarizedExperiment instances |
restrict-method | Intra range transformations of a GRanges or GRangesList object |
rglist | Squeeze the ranges out of a range-based object |
rowData | SummarizedExperiment instances |
rowData<- | SummarizedExperiment instances |
rowRanges | SummarizedExperiment instances |
rowRanges-method | SummarizedExperiment instances |
rowRanges<- | SummarizedExperiment instances |
rowRanges<--method | SummarizedExperiment instances |
score-method | GIntervalTree objects |
score-method | GRanges objects |
score-method | GRangesList objects |
score<--method | GRanges objects |
score<--method | GRangesList objects |
seqinfo-method | DelegatingGenomicRanges objects |
seqinfo-method | GIntervalTree objects |
seqinfo-method | GNCList objects |
seqinfo-method | GRanges objects |
seqinfo-method | GRangesList objects |
seqinfo-method | SummarizedExperiment instances |
seqinfo<--method | GRanges objects |
seqinfo<--method | GRangesList objects |
seqinfo<--method | SummarizedExperiment instances |
seqnames-method | DelegatingGenomicRanges objects |
seqnames-method | GIntervalTree objects |
seqnames-method | GNCList objects |
seqnames-method | GRanges objects |
seqnames-method | GRangesList objects |
seqnames-method | SummarizedExperiment instances |
seqnames<--method | GRanges objects |
seqnames<--method | GRangesList objects |
setdiff-method | Set operations on GRanges and GRangesList objects |
setops-methods | Set operations on GRanges and GRangesList objects |
ShallowData-class | SummarizedExperiment instances |
ShallowSimpleListAssays-class | SummarizedExperiment instances |
shift | Intra range transformations of a GRanges or GRangesList object |
shift-method | SummarizedExperiment instances |
shift-method | Intra range transformations of a GRanges or GRangesList object |
show-method | GIntervalTree objects |
show-method | GRanges objects |
show-method | GRangesList objects |
show-method | SummarizedExperiment instances |
SimpleGenomicRangesList-class | GenomicRangesList objects |
sort-method | Comparing and ordering genomic ranges |
sort-method | SummarizedExperiment instances |
sort.GenomicRanges | Comparing and ordering genomic ranges |
split-method | SummarizedExperiment instances |
start-method | GIntervalTree objects |
start-method | GNCList objects |
start-method | GRanges objects |
start-method | GRangesList objects |
start-method | SummarizedExperiment instances |
start<--method | GRanges objects |
start<--method | GRangesList objects |
start<--method | SummarizedExperiment instances |
strand-method | DelegatingGenomicRanges objects |
strand-method | GIntervalTree objects |
strand-method | GNCList objects |
strand-method | GRanges objects |
strand-method | GRangesList objects |
strand-method | SummarizedExperiment instances |
strand-method | Strand utilities |
strand-utils | Strand utilities |
strand<--method | GRanges objects |
strand<--method | GRangesList objects |
strand<--method | SummarizedExperiment instances |
strand<--method | Strand utilities |
subset-method | SummarizedExperiment instances |
subsetByOverlaps | Finding overlapping genomic ranges |
subsetByOverlaps-method | SummarizedExperiment instances |
subsetByOverlaps-method | Finding overlapping genomic ranges |
SummarizedExperiment | SummarizedExperiment instances |
SummarizedExperiment-class | SummarizedExperiment instances |
SummarizedExperiment-method | SummarizedExperiment instances |
tile-method | Tile a GenomicRanges object |
tile-methods | Tile a GenomicRanges object |
tileGenome | Put (virtual) tiles on a given genome |
trim-method | Intra range transformations of a GRanges or GRangesList object |
union-method | Set operations on GRanges and GRangesList objects |
update-method | DelegatingGenomicRanges objects |
updateObject-method | GRanges objects |
updateObject-method | GRangesList objects |
updateObject-method | SummarizedExperiment instances |
values-method | SummarizedExperiment instances |
values<--method | SummarizedExperiment instances |
width-method | GIntervalTree objects |
width-method | GNCList objects |
width-method | GRanges objects |
width-method | GRangesList 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 |
[-method | GIntervalTree objects |
[-method | GRanges objects |
[-method | GRangesList objects |
[-method | SummarizedExperiment instances |
[<--method | GRanges objects |
[<--method | GRangesList objects |
[<--method | SummarizedExperiment instances |
[[-method | SummarizedExperiment instances |
[[<--method | GRangesList objects |
[[<--method | SummarizedExperiment instances |