Package: GenomicAlignments 1.41.0

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]

# Install 'GenomicAlignments' in R:

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

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

On BioConductor:GenomicAlignments-1.41.0(bioc 3.20)GenomicAlignments-1.40.0(bioc 3.19)

bioconductor-package

121 exports 10.24 score 41 dependencies 522 dependents 134 mentions

Last updated 2 months agofrom:eb08522758

Exports:alphabetFrequencyFromBam as.data.frame as.data.frame.OverlapEncodings bindROWS cigar CIGAR_OPS cigarNarrow cigarOpTable cigarQNarrow cigarRangesAlongPairwiseSpace cigarRangesAlongQuerySpace cigarRangesAlongReferenceSpace cigarToRleList cigarWidthAlongPairwiseSpace cigarWidthAlongQuerySpace cigarWidthAlongReferenceSpace coerce countCompatibleOverlaps countDumpedAlignments coverage elementMetadata<-encodeOverlaps encodeOverlaps1 encoding encodingHalves end explodeCigarOpLengths explodeCigarOps extractAlignmentRangesOnReference extractQueryStartInTranscript extractSkippedExonRanks extractSpannedExonRanks extractSteppedExonRanks findCompatibleOverlaps findMateAlignment findOverlaps findSpliceOverlaps first flippedQuery flipQuery flushDumpedAlignments GAlignmentPairs GAlignments GAlignmentsList GappedReads getDumpedAlignments getListElement granges grglist IntersectionNotEmpty IntersectionStrict invertStrand is.unsorted isCompatibleWithSkippedExons isCompatibleWithSplicing isProperPair junctions last Lencoding levels levels.OverlapEncodings Lnjunc Loffset makeGAlignmentPairs mapFromAlignments mapToAlignments narrow NATURAL_INTRON_MOTIFS njunc order parallel_slot_names pcompare pileLettersAt pintersect pmapFromAlignments pmapToAlignments qnarrow qseq queryLoc2refLoc queryLocs2refLocs qwidth ranges rank readGAlignmentPairs readGAlignments readGAlignmentsList readGappedReads readSTARJunctions readTopHatJunctions relistToClass Rencoding rglist rname rname<-Rnjunc Roffset second selectEncodingWithCompatibleStrand seqinfo seqinfo<-seqlevelsInUse seqnames seqnames<-sequenceLayer show sort stackStringsFromBam stackStringsFromGAlignments start strand strand<-strandMode strandMode<-summarizeJunctions summarizeOverlaps Union update updateObject validCigar width windows

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 Rhtslib Rsamtools S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils XVector zlibbioc

An Introduction to the GenomicAlignments Package

Rendered fromGenomicAlignmentsIntroduction.Rnwusingutils::Sweaveon Jun 30 2024.

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

Counting reads with summarizeOverlaps

Rendered fromsummarizeOverlaps.Rnwusingutils::Sweaveon Jun 30 2024.

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

Overlap encodings

Rendered fromOverlapEncodings.Rnwusingutils::Sweaveon Jun 30 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 Jun 30 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CIGAR utility functions	cigar-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 object	coverage 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 model	encodeOverlaps 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 transcript	countCompatibleOverlaps findCompatibleOverlaps findCompatibleOverlaps,GAlignmentPairs,GRangesList-method findCompatibleOverlaps,GAlignments,GRangesList-method findCompatibleOverlaps-methods
Pairing the elements of a GAlignments object	countDumpedAlignments findMateAlignment flushDumpedAlignments getDumpedAlignments makeGAlignmentPairs
Finding overlapping genomic alignments	findOverlaps 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 events	findSpliceOverlaps findSpliceOverlaps,BamFile,ANY-method findSpliceOverlaps,character,ANY-method findSpliceOverlaps,GAlignmentPairs,GRangesList-method findSpliceOverlaps,GAlignments,GRangesList-method findSpliceOverlaps,GRangesList,GRangesList-method findSpliceOverlaps-methods
GAlignmentPairs objects	as.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 objects	as.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 objects	cigar,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 objects	c,GappedReads-method class:GappedReads GappedReads GappedReads-class qseq qseq,GappedReads-method qwidth,GappedReads-method
Intra range transformations of a GAlignments or GAlignmentsList object	intra-range-methods narrow,GappedReads-method qnarrow qnarrow,GAlignments-method qnarrow,GAlignmentsList-method qnarrow,GappedReads-method windows,GAlignments-method
Extract junctions from genomic alignments	junctions 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 alignments	coordinate-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 objects	as.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 positions	pileLettersAt
Reading genomic alignments from a file	readGAlignmentPairs 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 CIGARs	sequenceLayer
Set operations on GAlignments objects	pintersect pintersect,GAlignments,GRanges-method pintersect,GRanges,GAlignments-method setops-methods
Stack the read sequences stored in a GAlignments object or a BAM file	alphabetFrequencyFromBam stackStringsFromBam stackStringsFromGAlignments
Perform overlap queries between reads and genomic features	IntersectionNotEmpty 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