Package: GenomicTuples 1.41.1

Peter Hickey

GenomicTuples: Representation and Manipulation of Genomic Tuples

GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.

Authors:Peter Hickey [aut, cre], Marcin Cieslik [ctb], Hervé Pagès [ctb]

GenomicTuples_1.41.1.tar.gz
GenomicTuples_1.41.1.zip(r-4.5)GenomicTuples_1.41.1.zip(r-4.4)GenomicTuples_1.41.1.zip(r-4.3)
GenomicTuples_1.41.1.tgz(r-4.4-x86_64)GenomicTuples_1.41.1.tgz(r-4.4-arm64)GenomicTuples_1.41.1.tgz(r-4.3-x86_64)GenomicTuples_1.41.1.tgz(r-4.3-arm64)
GenomicTuples_1.41.1.tar.gz(r-4.5-noble)GenomicTuples_1.41.1.tar.gz(r-4.4-noble)
GenomicTuples_1.41.1.tgz(r-4.4-emscripten)GenomicTuples_1.41.1.tgz(r-4.3-emscripten)
GenomicTuples.pdf |GenomicTuples.html✨
GenomicTuples/json (API)
NEWS

# Install 'GenomicTuples' in R:
install.packages('GenomicTuples', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/petehaitch/genomictuples/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:GenomicTuples-1.41.0(bioc 3.21)GenomicTuples-1.40.0(bioc 3.20)

infrastructuredatarepresentationsequencing

5.48 score 4 stars 7 scripts 202 downloads 44 exports 20 dependencies

Last updated 8 days agofrom:ff46eeb868. Checks:OK: 1 WARNING: 5 ERROR: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-win-x86_64WARNINGNov 14 2024
R-4.5-linux-x86_64WARNINGNov 14 2024
R-4.4-win-x86_64WARNINGNov 14 2024
R-4.4-mac-x86_64WARNINGNov 14 2024
R-4.4-mac-aarch64WARNINGNov 14 2024
R-4.3-win-x86_64ERRORNov 14 2024
R-4.3-mac-x86_64ERRORNov 14 2024
R-4.3-mac-aarch64ERRORNov 14 2024

Exports:as.data.framecountOverlapscoveragedisjoindisjointBinsduplicatedduplicated.GTuplesfindOverlapsflankgapsgrangesgtlistgtuplesGTuplesGTuplesListintersectIPDis.unsortedisDisjointmatchnarrowOpsorderpcomparepgappintersectpromoterspsetdiffpunionreducerelistToClassresizerestrictselfmatchsetdiffshiftshowsizesortsort.GTuplestiletuplestuples<-union

Dependencies:askpassBiocGenericscurldata.tablegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitemimeopensslR6RcppS4VectorssysUCSC.utilsXVectorzlibbioc

GenomicTuples: Classes and Methods

Peter Hickey

Rendered fromGenomicTuplesIntroduction.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2016-05-26
Started: 2015-02-12

Readme and manuals

Help Manual

Help pageTopics
Representation and manipulation of genomic tuples.GenomicTuples-package
Finding overlapping genomic tuplescountOverlaps countOverlaps,GTuples,GTuples-method findOverlaps findOverlaps,GTuples,GTuples-method findOverlaps-methods overlapsAny overlapsAny,GTuples,GTuples-method subsetByOverlaps subsetByOverlaps,GTuples,GTuples-method
GTuples objects$,GTuples-method $<-,GTuples,numeric-method as.character,GTuples-method as.data.frame,GTuples-method as.factor,GTuples-method c,GTuples-method class:GTuples coerce,GRanges,GTuples-method elementMetadata<-,GTuples-method end,GTuples-method end<-,GTuples-method granges,GTuples-method GTuples GTuples-class IPD IPD,GTuples-method length,GTuples-method names,GTuples-method names<-,GTuples-method ranges,GTuples-method ranges<-,GTuples-method score,GTuples-method score<-,GTuples-method seqinfo,GTuples-method seqinfo<-,GTuples-method seqnames,GTuples-method seqnames<-,GTuples-method show,GTuples-method size size,GTuples-method start,GTuples-method start<-,GTuples-method strand,GTuples-method strand<-,GTuples-method tuples tuples,GTuples-method tuples<- tuples<-,GTuples-method updateObject,GTupless-method width,GTuples-method width<-,GTuples-method window,GTuples-method [,GTuples-method [<-,GTuples-method
Comparing and ordering genomic tuplesduplicated,GTuples-method duplicated.GTuples GTuples-comparison is.unsorted,GTuples-method match,GTuples,GTuples-method order,GTuples-method pcompare,GTuples,GTuples-method rank,GTuples-method selfmatch,GTuples-method sort,GTuples-method sort.GTuples
GTuplesList objectsclass:GTuplesList coerce,GTuplesList,data.frame-method coerce,GTuplesList,GRangesList-method coerce,GTuplesList,list-method elementMetadata,GTuplesList-method elementMetadata<-,GTuplesList-method end,GTuplesList-method end<-,GTuplesList-method GTuplesList GTuplesList-class IPD,GTuplesList-method ranges,GTuplesList-method ranges<-,GTuplesList-method relistToClass,GTuples-method score,GTuplesList-method score<-,GTuplesList-method seqinfo,GTuplesList-method seqinfo<-,GTuplesList-method seqnames,GTuplesList-method seqnames<-,GTuplesList-method size,GTuplesList-method start,GTuplesList-method start<-,GTuplesList-method strand,GTuplesList-method strand<-,GTuplesList,ANY-method strand<-,GTuplesList,character-method tuples,GTuplesList-method tuples<-,GTuplesList-method updateObject,GTuplesList-method width,GTuplesList-method width<-,GTuplesList-method [,GTuplesList,ANY-method [<-,GTuplesList,ANY,ANY,ANY-method [[<-,GTuplesList,ANY,ANY,ANY-method
Intra-tuple transformations of a GTuples or GTuplesLists objectintra-tuple-methods shift shift,GTuples-method shift,GTuplesList-method trim,GTuples-method
Finding the nearest genomic tuple/range neighbourdistance,GTuples,GTuples-method distanceToNearest,GTuples,GTuples-method distanceToNearest,GTuples,missing-method follow,GTuples,GTuples-method follow,GTuples,missing-method nearest,GTuples,GTuples-method nearest,GTuples,missing-method nearest-methods precede,GTuples,GTuples-method precede,GTuples,missing-method
Squeeze the tuples out of a tuples-based objectgtlist gtuples tuples-squeezers
Undefined methodscoverage,GTuples-method coverage,GTuplesList-method disjoin,GTuples-method disjoin,GTuplesList-method disjointBins,GTuples-method flank,GTuples-method flank,GTuplesList-method gaps,GTuples-method intersect,GTuples,GTuples-method isDisjoint,GTuples-method isDisjoint,GTuplesList-method narrow narrow,GTuples-method Ops,GTuples,numeric-method pgap,GTuples,GTuples-method pintersect,GTuples,GTuples-method pintersect,GTuples,GTuplesList-method pintersect,GTuplesList,GTuples-method pintersect,GTuplesList,GTuplesList-method promoters,GTuples-method promoters,GTuplesList-method psetdiff,GTuples,GTuples-method psetdiff,GTuples,GTuplesList-method psetdiff,GTuplesList,GTuplesList-method punion,GTuples,GTuples-method punion,GTuples,GTuplesList-method punion,GTuplesList,GTuples-method range,GTuples-method range,GTuplesList-method reduce,GTuples-method reduce,GTuplesList-method replaceROWS,NULL-method resize,GTuples-method resize,GTuplesList-method restrict,GTuplesList-method setdiff,GTuples,GTuples-method tile,GTuples-method union,GTuples,GTuples-method