Package: GenomicAlignments 1.43.0

Hervé Pagès

GenomicAlignments: Representation and manipulation of short genomic alignments

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Authors:Hervé Pagès [aut, cre], Valerie Obenchain [aut], Martin Morgan [aut], Fedor Bezrukov [ctb], Robert Castelo [ctb], Halimat C. Atanda [ctb]

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GenomicAlignments.pdf |GenomicAlignments.html✨
GenomicAlignments/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/bioconductor/genomicalignments/issues

On BioConductor:GenomicAlignments-1.43.0(bioc 3.21)GenomicAlignments-1.42.0(bioc 3.20)

infrastructuredataimportgeneticssequencingrnaseqsnpcoveragealignmentimmunooncologybioconductor-packagecore-package

15.49 score 9 stars 530 packages 3.0k scripts 46k downloads 134 mentions 121 exports 42 dependencies

Last updated 1 months agofrom:db308fe009. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-win-x86_64NOTENov 29 2024
R-4.5-linux-x86_64NOTENov 29 2024
R-4.4-win-x86_64NOTENov 29 2024
R-4.4-mac-x86_64NOTENov 29 2024
R-4.4-mac-aarch64NOTENov 29 2024
R-4.3-win-x86_64NOTENov 29 2024
R-4.3-mac-x86_64NOTENov 29 2024
R-4.3-mac-aarch64NOTENov 29 2024

Exports:alphabetFrequencyFromBamas.data.frameas.data.frame.OverlapEncodingsbindROWScigarCIGAR_OPScigarNarrowcigarOpTablecigarQNarrowcigarRangesAlongPairwiseSpacecigarRangesAlongQuerySpacecigarRangesAlongReferenceSpacecigarToRleListcigarWidthAlongPairwiseSpacecigarWidthAlongQuerySpacecigarWidthAlongReferenceSpacecoercecountCompatibleOverlapscountDumpedAlignmentscoverageelementMetadata<-encodeOverlapsencodeOverlaps1encodingencodingHalvesendexplodeCigarOpLengthsexplodeCigarOpsextractAlignmentRangesOnReferenceextractQueryStartInTranscriptextractSkippedExonRanksextractSpannedExonRanksextractSteppedExonRanksfindCompatibleOverlapsfindMateAlignmentfindOverlapsfindSpliceOverlapsfirstflippedQueryflipQueryflushDumpedAlignmentsGAlignmentPairsGAlignmentsGAlignmentsListGappedReadsgetDumpedAlignmentsgetListElementgrangesgrglistIntersectionNotEmptyIntersectionStrictinvertStrandis.unsortedisCompatibleWithSkippedExonsisCompatibleWithSplicingisProperPairjunctionslastLencodinglevelslevels.OverlapEncodingsLnjuncLoffsetmakeGAlignmentPairsmapFromAlignmentsmapToAlignmentsnarrowNATURAL_INTRON_MOTIFSnjuncorderparallel_slot_namespcomparepileLettersAtpintersectpmapFromAlignmentspmapToAlignmentsqnarrowqseqqueryLoc2refLocqueryLocs2refLocsqwidthrangesrankreadGAlignmentPairsreadGAlignmentsreadGAlignmentsListreadGappedReadsreadSTARJunctionsreadTopHatJunctionsrelistToClassRencodingrglistrnamername<-RnjuncRoffsetsecondselectEncodingWithCompatibleStrandseqinfoseqinfo<-seqlevelsInUseseqnamesseqnames<-sequenceLayershowsortstackStringsFromBamstackStringsFromGAlignmentsstartstrandstrand<-strandModestrandMode<-summarizeJunctionssummarizeOverlapsUnionupdateupdateObjectvalidCigarwidthwindows

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RhtslibRsamtoolsS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

An Introduction to the GenomicAlignments Package

Rendered fromGenomicAlignmentsIntroduction.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2018-07-17
Started: 2016-02-09

Counting reads with summarizeOverlaps

Rendered fromsummarizeOverlaps.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2024-02-13
Started: 2013-11-12

Overlap encodings

Rendered fromOverlapEncodings.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2018-02-10
Started: 2014-01-18

Working with aligned nucleotides (WORK-IN-PROGRESS!)

Hervé Pagès, Halimat C. Atanda

Rendered fromWorkingWithAlignedNucleotides.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-03-25
Started: 2024-03-25

Readme and manuals

Help Manual

Help pageTopics
CIGAR utility functionscigar-utils cigarNarrow cigarOpTable cigarQNarrow cigarRangesAlongPairwiseSpace cigarRangesAlongQuerySpace cigarRangesAlongReferenceSpace cigarToRleList cigarWidthAlongPairwiseSpace cigarWidthAlongQuerySpace cigarWidthAlongReferenceSpace CIGAR_OPS explodeCigarOpLengths explodeCigarOps extractAlignmentRangesOnReference queryLoc2refLoc queryLocs2refLocs validCigar
Coverage of a GAlignments, GAlignmentPairs, or GAlignmentsList objectcoverage coverage,BamFile-method coverage,character-method coverage,GAlignmentPairs-method coverage,GAlignments-method coverage,GAlignmentsList-method coverage-methods
Encode the overlaps between RNA-seq reads and the transcripts of a gene modelencodeOverlaps encodeOverlaps,GRangesList,GRangesList-method encodeOverlaps,IntegerRanges,IntegerRangesList-method encodeOverlaps,IntegerRangesList,IntegerRanges-method encodeOverlaps,IntegerRangesList,IntegerRangesList-method encodeOverlaps-methods encodeOverlaps1 extractQueryStartInTranscript extractSkippedExonRanks extractSkippedExonRanks,character-method extractSkippedExonRanks,factor-method extractSkippedExonRanks,OverlapEncodings-method extractSpannedExonRanks extractSpannedExonRanks,character-method extractSpannedExonRanks,factor-method extractSpannedExonRanks,OverlapEncodings-method extractSteppedExonRanks extractSteppedExonRanks,character-method extractSteppedExonRanks,factor-method extractSteppedExonRanks,OverlapEncodings-method flipQuery isCompatibleWithSkippedExons isCompatibleWithSkippedExons,character-method isCompatibleWithSkippedExons,factor-method isCompatibleWithSkippedExons,OverlapEncodings-method selectEncodingWithCompatibleStrand
Finding hits between reads and transcripts that are _compatible_ with the splicing of the transcriptcountCompatibleOverlaps findCompatibleOverlaps findCompatibleOverlaps,GAlignmentPairs,GRangesList-method findCompatibleOverlaps,GAlignments,GRangesList-method findCompatibleOverlaps-methods
Pairing the elements of a GAlignments objectcountDumpedAlignments findMateAlignment flushDumpedAlignments getDumpedAlignments makeGAlignmentPairs
Finding overlapping genomic alignmentsfindOverlaps findOverlaps,GAlignmentPairs,GAlignmentPairs-method findOverlaps,GAlignmentPairs,Vector-method findOverlaps,GAlignments,GAlignments-method findOverlaps,GAlignments,Vector-method findOverlaps,GAlignmentsList,GAlignmentsList-method findOverlaps,GAlignmentsList,Vector-method findOverlaps,Vector,GAlignmentPairs-method findOverlaps,Vector,GAlignments-method findOverlaps,Vector,GAlignmentsList-method findOverlaps-methods
Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice eventsfindSpliceOverlaps findSpliceOverlaps,BamFile,ANY-method findSpliceOverlaps,character,ANY-method findSpliceOverlaps,GAlignmentPairs,GRangesList-method findSpliceOverlaps,GAlignments,GRangesList-method findSpliceOverlaps,GRangesList,GRangesList-method findSpliceOverlaps-methods
GAlignmentPairs objectsas.data.frame,GAlignmentPairs-method bindROWS,GAlignmentPairs-method class:GAlignmentPairs coerce,GAlignmentPairs,DataFrame-method coerce,GAlignmentPairs,GAlignments-method coerce,GAlignmentPairs,GRanges-method coerce,GAlignmentPairs,GRangesList-method coerce,GAlignmentPairs,IntegerRanges-method first first,GAlignmentPairs-method GAlignmentPairs GAlignmentPairs-class granges,GAlignmentPairs-method grglist,GAlignmentPairs-method invertStrand,GAlignmentPairs-method isProperPair isProperPair,GAlignmentPairs-method last last,GAlignmentPairs-method names,GAlignmentPairs-method names<-,GAlignmentPairs-method njunc,GAlignmentPairs-method parallel_slot_names,GAlignmentPairs-method ranges,GAlignmentPairs-method second second,GAlignmentPairs-method seqinfo,GAlignmentPairs-method seqinfo<-,GAlignmentPairs-method seqlevelsInUse,GAlignmentPairs-method seqnames,GAlignmentPairs-method show,GAlignmentPairs-method strand,GAlignmentPairs-method strandMode strandMode,GAlignmentPairs-method strandMode<- strandMode<-,GAlignmentPairs-method unlist,GAlignmentPairs-method updateObject,GAlignmentPairs-method [[,GAlignmentPairs,ANY,ANY-method
GAlignments objectsas.data.frame,GAlignments-method bindROWS,GAlignments-method cigar cigar,GAlignments-method class:GAlignments coerce,GAlignments,DataFrame-method coerce,GAlignments,GRanges-method coerce,GAlignments,GRangesList-method coerce,GAlignments,IntegerRanges-method coerce,GAlignments,IntegerRangesList-method coerce,GenomicRanges,GAlignments-method GAlignments GAlignments-class getListElement,GAlignments-method granges,GAlignments-method grglist,GAlignments-method is.unsorted,GAlignments-method names,GAlignments-method names<-,GAlignments-method njunc njunc,GAlignments-method order,GAlignments-method parallel_slot_names,GAlignments-method pcompare,GAlignments,GAlignments-method qwidth qwidth,GAlignments-method ranges,GAlignments-method rank,GAlignments-method rglist,GAlignments-method rname rname,GAlignments-method rname<- rname<-,GAlignments-method seqinfo,GAlignments-method seqinfo<-,GAlignments-method seqnames,GAlignments-method seqnames<-,GAlignments-method show,GAlignments-method sort,GAlignments-method start,GAlignments-method strand,GAlignments-method strand<-,GAlignments,ANY-method update,GAlignments-method updateObject,GAlignments-method width,GAlignments-method
GAlignmentsList objectscigar,GAlignmentsList-method class:GAlignmentsList coerce,GAlignmentPairs,GAlignmentsList-method coerce,GAlignmentsList,GAlignmentPairs-method coerce,GAlignmentsList,GRanges-method coerce,GAlignmentsList,GRangesList-method coerce,GAlignmentsList,IntegerRanges-method coerce,GAlignmentsList,IntegerRangesList-method coerce,list,GAlignmentsList-method elementMetadata,GAlignmentsList-method elementMetadata<-,GAlignmentsList-method GAlignmentsList GAlignmentsList-class granges,GAlignmentsList-method grglist,GAlignmentsList-method names,GAlignmentsList-method names<-,GAlignmentsList-method njunc,GAlignmentsList-method qwidth,GAlignmentsList-method ranges,GAlignmentsList-method relistToClass,GAlignments-method rglist,GAlignmentsList-method rname,GAlignmentsList-method rname<-,GAlignmentsList-method seqinfo,GAlignmentsList-method seqinfo<-,GAlignmentsList-method seqnames,GAlignmentsList-method seqnames<-,GAlignmentsList-method show,GAlignmentsList-method strand,GAlignmentsList-method strand<-,GAlignmentsList,character-method strand<-,GAlignmentsList-method
(Legacy) GappedReads objectsc,GappedReads-method class:GappedReads GappedReads GappedReads-class qseq qseq,GappedReads-method qwidth,GappedReads-method
Intra range transformations of a GAlignments or GAlignmentsList objectintra-range-methods narrow,GappedReads-method qnarrow qnarrow,GAlignments-method qnarrow,GAlignmentsList-method qnarrow,GappedReads-method windows,GAlignments-method
Extract junctions from genomic alignmentsjunctions junctions,GAlignmentPairs-method junctions,GAlignments-method junctions,GAlignmentsList-method junctions-methods NATURAL_INTRON_MOTIFS readSTARJunctions readTopHatJunctions summarizeJunctions
Map range coordinates between reads and genome space using CIGAR alignmentscoordinate-mapping-methods mapFromAlignments mapFromAlignments,GenomicRanges,GAlignments-method mapFromAlignments,IntegerRanges,GAlignments-method mapToAlignments mapToAlignments,GenomicRanges,GAlignments-method mapToAlignments,IntegerRanges,GAlignments-method pmapFromAlignments pmapFromAlignments,GenomicRanges,GAlignments-method pmapFromAlignments,IntegerRanges,GAlignments-method pmapToAlignments pmapToAlignments,GenomicRanges,GAlignments-method pmapToAlignments,IntegerRanges,GAlignments-method
OverlapEncodings objectsas.data.frame,OverlapEncodings-method as.data.frame.OverlapEncodings class:OverlapEncodings encoding,OverlapEncodings-method encodingHalves encodingHalves,character-method encodingHalves,factor-method encodingHalves,OverlapEncodings-method flippedQuery flippedQuery,OverlapEncodings-method isCompatibleWithSplicing isCompatibleWithSplicing,character-method isCompatibleWithSplicing,factor-method isCompatibleWithSplicing,OverlapEncodings-method Lencoding levels,OverlapEncodings-method levels.OverlapEncodings Lnjunc Loffset Loffset,OverlapEncodings-method njunc,ANY-method OverlapEncodings OverlapEncodings-class parallel_slot_names,OverlapEncodings-method Rencoding Rnjunc Roffset Roffset,OverlapEncodings-method show,OverlapEncodings-method
Pile the letters of a set of aligned reads on top of a set of genomic positionspileLettersAt
Reading genomic alignments from a filereadGAlignmentPairs readGAlignmentPairs,BamFile-method readGAlignmentPairs,character-method readGAlignments readGAlignments,BamFile-method readGAlignments,BamViews-method readGAlignments,character-method readGAlignmentsList readGAlignmentsList,BamFile-method readGAlignmentsList,character-method readGappedReads readGappedReads,BamFile-method readGappedReads,character-method
Lay read sequences alongside the reference space, using their CIGARssequenceLayer
Set operations on GAlignments objectspintersect pintersect,GAlignments,GRanges-method pintersect,GRanges,GAlignments-method setops-methods
Stack the read sequences stored in a GAlignments object or a BAM filealphabetFrequencyFromBam stackStringsFromBam stackStringsFromGAlignments
Perform overlap queries between reads and genomic featuresIntersectionNotEmpty IntersectionStrict summarizeOverlaps summarizeOverlaps,BamViews,missing-method summarizeOverlaps,GRanges,BamFile-method summarizeOverlaps,GRanges,BamFileList-method summarizeOverlaps,GRanges,character-method summarizeOverlaps,GRanges,GAlignmentPairs-method summarizeOverlaps,GRanges,GAlignments-method summarizeOverlaps,GRanges,GAlignmentsList-method summarizeOverlaps,GRanges,GRanges-method summarizeOverlaps,GRanges,GRangesList-method summarizeOverlaps,GRangesList,BamFile-method summarizeOverlaps,GRangesList,BamFileList-method summarizeOverlaps,GRangesList,character-method summarizeOverlaps,GRangesList,GAlignmentPairs-method summarizeOverlaps,GRangesList,GAlignments-method summarizeOverlaps,GRangesList,GAlignmentsList-method summarizeOverlaps,GRangesList,GRanges-method summarizeOverlaps,GRangesList,GRangesList-method summarizeOverlaps-methods Union