Bioconductor/GenomicRanges
Representation and manipulation of genomic intervals

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Search the Bioconductor/GenomicRanges package
Vignettes
Functions
522
Source code
46
Man pages
25
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Bioconductor/GenomicRanges: Representation and manipulation of genomic intervals
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API

API for Bioconductor/GenomicRanges
Representation and manipulation of genomic intervals

Global functions
$,GenomicRanges-method Man page
$<-,GenomicRanges-method Man page
.DollarNames.GenomicRanges Source code
.GenomicRanges_as_integer_quads Source code
.GenomicRanges_findPrecedeFollow Source code
.GenomicRanges_promoters Source code
.Hits Source code
.aggregated_sum Source code
.as.data.frame.GPos Source code
.as_list_of_GRanges Source code
.checkParms Source code
.check_GenomicRanges_for_coercion_to_GPos Source code
.collect_prefixes Source code
.compute_promoter_ranges Source code
.distanceToNearest Source code
.duplicated.GenomicRanges Source code
.extract_groups_from_GenomicRanges Source code
.fast_binary_mendoapply Source code
.filterHits Source code
.findNearest_distance Source code
.findPrecedeFollow_pmin Source code
.find_GRanges_cols Source code
.find_seqnames_col Source code
.find_start_end_cols Source code
.find_strand_col Source code
.find_width_col Source code
.fix_inner_revmap_mcol Source code
.from_ANY_to_StitchedGPos Source code
.from_ANY_to_UnstitchedGPos Source code
.from_GPos_to_naked_character_matrix_for_display Source code
.from_GenomicRanges_to_CompressedIRangesList Source code
.from_GenomicRanges_to_naked_character_matrix_for_display Source code
.from_List_to_CompressedGRangesList Source code
.from_List_to_SimpleGRangesList Source code
.from_RleViews_to_IRanges_with_score_and_view_mcols Source code
.from_Seqinfo_to_GRanges Source code
.from_character_to_GRanges Source code
.from_factor_to_GRanges Source code
.from_list_to_CompressedGRangesList Source code
.from_list_to_SimpleGRangesList Source code
.get_GPos_version Source code
.get_GRanges_version Source code
.get_circle_length Source code
.get_data_frame_col_as_numeric Source code
.get_relative_ends Source code
.get_relative_starts Source code
.invert_strand_factor Source code
.make_breakpoints_for_cut_last_tile_in_chrom Source code
.make_spaceid Source code
.maxEndPerGRangesSequence Source code
.minStartPerGRangesSequence Source code
.nearest Source code
.nearestDistance Source code
.nearestKNeighbors Source code
.nearestKNeighbors_all_k Source code
.new_stitched_GRanges Source code
.nextCheckConstraintSignatures Source code
.normBounds Source code
.normalize_seqnames_replacement_value Source code
.normarg_field Source code
.normarg_shift_or_weight Source code
.onUnload Source code
.orderNumeric Source code
.overlapwidth Source code
.pad_with_zeros Source code
.paste12 Source code
.pcompare_GenomicRanges Source code
.pintersect_GRangesList_GRanges Source code
.pintersect_GRanges_GRanges Source code
.print_levels Source code
.restrictRngs Source code
.sBracketReplaceGRList Source code
.sBracketSubsetGRList Source code
.selectClosestMethod1 Source code
.show_GRangesFactor Source code
.sort.GRangesList Source code
.sort.GenomicRanges Source code
.subset_by_GenomicRanges Source code
.superimpose_breakpoints Source code
.test Source code
.translate_revmap Source code
.try_to_coerce_to_GRanges_first Source code
.unsupported_intersect Source code
.unsupported_setdiff Source code
.unsupported_union Source code
.valid.GRanges Source code
.valid.GRanges.mcols Source code
.valid.GRanges.ranges Source code
.valid.GenomicRanges Source code
.valid.GenomicRanges.mcols Source code
.valid.GenomicRanges.ranges Source code
.valid.GenomicRanges.seqnames Source code
.valid.GenomicRanges.strand Source code
.valid.GenomicRangesList Source code
.valid.GenomicRangesList.mcols Source code
.validate_GPos Source code
CompressedGRangesList Man page
CompressedGRangesList-class Man page
CompressedGenomicRangesList Man page
CompressedGenomicRangesList-class Man page
Constraint Man page
Constraint-class Man page
Constraint_OR_NULL Man page
Constraint_OR_NULL-class Man page
Constraints Man page
DelegatingGenomicRanges-class Man page Man page
FactorToClass,GRanges-method Man page
GNCList Man page Source code
GNCList-class Man page
GPos Man page Source code
GPos-class Man page
GRanges Man page Man page Source code
GRanges-class Man page
GRangesFactor Man page Source code
GRangesFactor-class Man page
GRangesList Man page Source code
GRangesList-class Man page
GenomicPos Man page
GenomicPos-class Man page
GenomicRanges Man page
GenomicRanges-class Man page
GenomicRanges-comparison Man page
GenomicRangesList Man page
GenomicRangesList-class Man page
GenomicRanges_OR_GRangesList Man page
GenomicRanges_OR_GRangesList-class Man page
GenomicRanges_OR_GenomicRangesList Man page
GenomicRanges_OR_GenomicRangesList-class Man page
GenomicRanges_OR_missing-class Man page
IRanges_OR_IPos Man page
IRanges_OR_IPos-class Man page
SimpleGRangesList Man page
SimpleGRangesList-class Man page
SimpleGenomicRangesList Man page
SimpleGenomicRangesList-class Man page
StitchedGPos Man page
StitchedGPos-class Man page
UnstitchedGPos Man page
UnstitchedGPos-class Man page
[,CompressedGRangesList,ANY-method Man page
[,list_OR_List,GenomicRanges-method Man page
[<-,CompressedGRangesList,ANY,ANY,ANY-method Man page
[<-,CompressedGRangesList,ANY-method Man page
[<-,CompressedGRangesList-method Man page
absoluteRanges Man page Source code
allCompatibleSeqnamesAndStrand Source code
as.character,GenomicRanges-method Man page
as.data.frame,GPos-method Man page
as.data.frame,GenomicRanges-method Man page
as.data.frame.GPos Man page Source code
as.factor,GenomicRanges-method Man page
bindAsGRanges Man page Source code
bindROWS,GenomicRanges-method Man page
binnedAverage Man page Source code
checkConstraint Man page
class:CompressedGRangesList Man page
class:CompressedGenomicRangesList Man page
class:Constraint Man page
class:Constraint_OR_NULL Man page
class:DelegatingGenomicRanges Man page Man page
class:GNCList Man page
class:GPos Man page
class:GRanges Man page
class:GRangesFactor Man page
class:GRangesList Man page
class:GenomicPos Man page
class:GenomicRanges Man page
class:GenomicRangesList Man page
class:GenomicRanges_OR_GRangesList Man page
class:GenomicRanges_OR_GenomicRangesList Man page
class:IRanges_OR_IPos Man page
class:SimpleGRangesList Man page
class:SimpleGenomicRangesList Man page
class:StitchedGPos Man page
class:UnstitchedGPos Man page
coerce,ANY,GPos-method Man page
coerce,ANY,GRangesFactor-method Man page
coerce,ANY,GenomicRanges-method Man page
coerce,ANY,StitchedGPos-method Man page
coerce,ANY,UnstitchedGPos-method Man page
coerce,CompressedGRangesList,CompressedIRangesList-method Man page
coerce,CompressedGRangesList,IRangesList-method Man page
coerce,CompressedGRangesList,IntegerRangesList-method Man page
coerce,DataFrame,GRanges-method Man page
coerce,Factor,GRanges-method Man page
coerce,GNCList,GRanges-method Man page
coerce,GRanges,GPos-method Man page
coerce,GRanges,StitchedGPos-method Man page
coerce,GRanges,UnstitchedGPos-method Man page
coerce,GenomicRanges,CompressedIRangesList-method Man page
coerce,GenomicRanges,GNCList-method Man page
coerce,GenomicRanges,GRanges-method Man page
coerce,GenomicRanges,Grouping-method Man page
coerce,GenomicRanges,IRangesList-method Man page
coerce,GenomicRanges,IntegerRangesList-method Man page
coerce,GenomicRangesList,SimpleGRangesList-method Man page
coerce,IntegerRangesList,GRanges-method Man page
coerce,List,CompressedGRangesList-method Man page
coerce,List,GRangesList-method Man page
coerce,List,SimpleGRangesList-method Man page
coerce,RleList,GRanges-method Man page
coerce,RleViewsList,GRanges-method Man page
coerce,Seqinfo,GRanges-method Man page
coerce,Seqinfo,IntegerRangesList-method Man page
coerce,SimpleGenomicRangesList,SimpleGRangesList-method Man page
coerce,SimpleList,SimpleGRangesList-method Man page
coerce,StitchedGPos,GRanges-method Man page
coerce,UnstitchedGPos,GRanges-method Man page
coerce,character,GRanges-method Man page
coerce,data.frame,GRanges-method Man page
coerce,factor,GRanges-method Man page
coerce,list,CompressedGRangesList-method Man page
coerce,list,GRangesList-method Man page
coerce,list,SimpleGRangesList-method Man page
combine_seqinfo_from_GenomicRanges_objects Source code
compatibleSeqnames Source code
compatibleStrand Source code
concatenate_GenomicRanges_objects Source code
constraint Man page
constraint<- Man page
countOverlaps Man page
countOverlaps,GenomicRanges,GenomicRanges-method Man page
countOverlaps_GenomicRanges Source code
coverage Man page
coverage,GRangesList-method Man page
coverage,GenomicRanges-method Man page
coverage,StitchedGPos-method Man page
coverage-methods Man page
deconstructGRLintoGR Source code
deconstructGRintoRGL Source code
disjoin Man page
disjoin,GRangesList-method Man page
disjoin,GenomicRanges-method Man page
disjointBins Man page
disjointBins,GenomicRanges-method Man page
distance Man page
distance,GenomicRanges,GenomicRanges-method Man page
distanceToNearest Man page
distanceToNearest,GenomicRanges,GenomicRanges-method Man page
distanceToNearest,GenomicRanges,missing-method Man page
duplicated,GenomicRanges-method Man page
duplicated.GenomicRanges Man page Source code
elementMetadata,GenomicRangesList-method Man page
elementMetadata<-,CompressedGenomicRangesList-method Man page
end,GNCList-method Man page
end,GRangesFactor-method Man page
end<-,CompressedGenomicRangesList-method Man page
end<-,GenomicRanges-method Man page
extraColumnSlots Source code
extraColumnSlotsAsDF Source code
extractROWS,GenomicRangesList,ANY-method Man page
findOverlaps Man page
findOverlaps,GRangesList,GRangesList-method Man page
findOverlaps,GRangesList,GenomicRanges-method Man page
findOverlaps,GenomicRanges,GRangesList-method Man page
findOverlaps,GenomicRanges,GenomicRanges-method Man page
findOverlaps-methods Man page
findOverlaps_GNCList Source code
findOverlaps_GenomicRanges Source code
flank Man page
flank,GenomicRanges-method Man page
follow Man page
follow,GenomicRanges,GenomicRanges-method Man page
follow,GenomicRanges,missing-method Man page
follows Source code
from_GPos_to_GRanges Man page Source code
gaps Man page
gaps,GenomicRanges-method Man page
genomic-range-squeezers Man page
genomicvariables Man page
genomicvars Man page
getListElement,GenomicRanges-method Man page
getListElement,GenomicRangesList-method Man page
get_GenomicRangesList_mcols Source code
get_out_of_bound_index Source code
granges Man page
granges,GNCList-method Man page
granges,GRangesFactor-method Man page
granges,GenomicRanges-method Man page
grglist Man page
grglist,Pairs-method Man page
hasHead Source code
inter-range-methods Man page
intersect Man page
intersect,GRangesList,GRangesList-method Man page
intersect,GenomicRanges,GenomicRanges-method Man page
intersect,GenomicRanges,Vector-method Man page
intersect,Vector,GenomicRanges-method Man page
intra-range-methods Man page
invertStrand,NULL-method Man page
invertStrand,Rle-method Man page
invertStrand,RleList-method Man page
invertStrand,character-method Man page
invertStrand,factor-method Man page
invertStrand,integer-method Man page
invertStrand,logical-method Man page
is.unsorted,GenomicRanges-method Man page
isDisjoint Man page
isDisjoint,GRangesList-method Man page
isDisjoint,GenomicRanges-method Man page
isDisjoint,StitchedGPos-method Man page
isSmallGenome Man page Source code
length,GNCList-method Man page
length,GenomicRanges-method Man page
length,GenomicRangesList-method Man page
makeGRangesFromDataFrame Man page Source code
makeGRangesListFromDataFrame Man page Source code
makeGRangesListFromFeatureFragments Man page Source code
make_out_of_bound_warning_msg Source code
match,GenomicRanges,GenomicRanges-method Man page
mcolAsRleList Man page Source code
names,GNCList-method Man page
names,GenomicRanges-method Man page
names,GenomicRangesList-method Man page
names<-,GenomicRanges-method Man page
names<-,GenomicRangesList-method Man page
narrow Man page
narrow,GenomicRanges-method Man page
nearest Man page
nearest,GenomicRanges,GenomicRanges-method Man page
nearest,GenomicRanges,missing-method Man page
nearest-methods Man page
nearestKNeighbors Man page
nearestKNeighbors,GenomicRanges,GenomicRanges-method Man page
nearestKNeighbors,GenomicRanges,missing-method Man page
new_GRanges Source code
normalize_strand_replacement_value Source code
normarg_list_of_integers Source code
normarg_seqinfo1 Source code
normarg_seqinfo2 Source code
normarg_seqlengths Source code
normarg_seqnames1 Source code
normarg_seqnames2 Source code
normarg_strand Source code
order,GenomicRanges-method Man page
order_GenomicRanges Source code
overlapsAny Man page
parallel_slot_names,GRanges-method Man page
pcompare Man page
pcompare,GenomicRanges,GenomicRanges-method Man page
pgap Man page
pgap,GRanges,GRanges-method Man page
phicoef Man page Source code
pintersect Man page
pintersect,GRanges,GRanges-method Man page
pintersect,GRanges,GRangesList-method Man page
pintersect,GRangesList,GRanges-method Man page
pos,GPos-method Man page
pos,GRangesFactor-method Man page
precede Man page
precede,GenomicRanges,GenomicRanges-method Man page
precede,GenomicRanges,missing-method Man page
precedes Source code
promoters Man page
promoters,GenomicRanges-method Man page
psetdiff Man page
psetdiff,GRanges,GRanges-method Man page
psetdiff,GRanges,GRangesList-method Man page
punion Man page
punion,GRanges,GRanges-method Man page
punion,GRanges,GRangesList-method Man page
punion,GRangesList,GRanges-method Man page
range Man page
range,GRangesList-method Man page
range,GenomicRanges-method Man page
range,StitchedGPos-method Man page
ranges,CompressedGRangesList-method Man page
ranges,DelegatingGenomicRanges-method Man page
ranges,GNCList-method Man page
ranges,GRanges-method Man page
ranges,GRangesFactor-method Man page
ranges<-,CompressedGRangesList-method Man page
ranges<-,GenomicRanges-method Man page
rank,GenomicRanges-method Man page
reconstructGRLfromGR Source code
reconstructGRfromRGL Source code
reduce Man page
reduce,GRangesList-method Man page
reduce,GenomicRanges-method Man page
relativeRanges Man page Source code
relevelSeqnamesForMatch Source code
relistToClass,GRanges-method Man page
resize Man page
resize,GenomicRanges-method Man page
restrict Man page
restrict,GenomicRanges-method Man page
score,GenomicRanges-method Man page
score,GenomicRangesList-method Man page
score<-,GenomicRanges-method Man page
score<-,GenomicRangesList-method Man page
selfmatch,GenomicRanges-method Man page
seqinfo,CompressedGenomicRangesList-method Man page
seqinfo,DelegatingGenomicRanges-method Man page
seqinfo,GNCList-method Man page
seqinfo,GRanges-method Man page
seqinfo,GRangesFactor-method Man page
seqinfo,GenomicRangesList-method Man page
seqinfo,List-method Man page
seqinfo<-,CompressedGenomicRangesList-method Man page
seqinfo<-,GenomicRanges-method Man page
seqinfo<-,List-method Man page
seqnames,DelegatingGenomicRanges-method Man page
seqnames,GNCList-method Man page
seqnames,GRanges-method Man page
seqnames,GRangesFactor-method Man page
seqnames,GenomicRangesList-method Man page
seqnames<-,CompressedGenomicRangesList-method Man page
seqnames<-,GenomicRanges-method Man page
set_CompressedGenomicRangesList_mcols Source code
set_CompressedGenomicRangesList_seqinfo Source code
set_CompressedGenomicRangesList_seqnames Source code
set_CompressedGenomicRangesList_strand Source code
set_GenomicRanges_seqinfo Source code
setdiff Man page
setdiff,GRangesList,GRangesList-method Man page
setdiff,GenomicRanges,GenomicRanges-method Man page
setdiff,GenomicRanges,Vector-method Man page
setdiff,Vector,GenomicRanges-method Man page
setops-methods Man page
shift Man page
shift,GenomicRanges-method Man page
show,GPos-method Man page
show,GRangesFactor-method Man page
show,GenomicRanges-method Man page
show,GenomicRangesList-method Man page
show_GPos Source code
show_GenomicRanges Source code
show_GenomicRangesList Source code
slidingWindows Man page
slidingWindows,GenomicRanges-method Man page
sort,CompressedGRangesList-method Man page
sort,GRangesList-method Man page
sort,GenomicRanges-method Man page
sort.GRangesList Man page Source code
sort.GenomicRanges Man page Source code
start,GNCList-method Man page
start,GRangesFactor-method Man page
start,GenomicRanges-method Man page
start<-,CompressedGenomicRangesList-method Man page
start<-,GenomicRanges-method Man page
stitch_GenomicRanges Source code
stitch_StitchedGPos Source code
strand,DataFrame-method Man page
strand,DelegatingGenomicRanges-method Man page
strand,GNCList-method Man page
strand,GRanges-method Man page
strand,GRangesFactor-method Man page
strand,GenomicRangesList-method Man page
strand,NULL-method Man page
strand,Rle-method Man page
strand,RleList-method Man page
strand,character-method Man page
strand,factor-method Man page
strand,integer-method Man page
strand,logical-method Man page
strand,missing-method Man page
strand-utils Man page
strand<-,CompressedGenomicRangesList,ANY-method Man page
strand<-,CompressedGenomicRangesList,character-method Man page
strand<-,DataFrame,ANY-method Man page
strand<-,GenomicRanges,ANY-method Man page
subsetByOverlaps Man page
subtract Man page
subtract,GenomicRanges,GenomicRanges-method Man page
subtract-methods Man page
summary,GPos-method Man page
summary,GenomicRanges-method Man page
summary.GPos Man page
summary.GenomicRanges Man page
terminators Man page
terminators,GenomicRanges-method Man page
tile Man page
tile,GenomicRanges-method Man page
tile-methods Man page
tileGenome Man page Source code
trim Man page
trim,GRangesList-method Man page
trim,GenomicRanges-method Man page
union Man page
union,GRangesList,GRangesList-method Man page
union,GenomicRanges,GenomicRanges-method Man page
union,GenomicRanges,Vector-method Man page
union,Vector,GenomicRanges-method Man page
unlist,GenomicRangesList-method Man page
unsafe.transcriptLocs2refLocs Source code
unsafe.transcriptWidths Source code
update,DelegatingGenomicRanges-method Man page
update,GRanges-method Man page
updateObject,GPos-method Man page
updateObject,GRanges-method Man page
updateObject,GenomicRangesList-method Man page
update_ranges,GenomicRanges-method Man page
valid.GenomicRanges.seqinfo Source code
width,GNCList-method Man page
width,GRangesFactor-method Man page
width,GenomicRanges-method Man page
width<-,CompressedGenomicRangesList-method Man page
width<-,GenomicRanges-method Man page
Bioconductor/GenomicRanges documentation built on March 19, 2024, 12:39 p.m.

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