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.

AuthorHervé Pagès, Valerie Obenchain, Martin Morgan
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.10.0

View on Bioconductor

Files in this package

GenomicAlignments/DESCRIPTION
GenomicAlignments/NAMESPACE
GenomicAlignments/NEWS
GenomicAlignments/R
GenomicAlignments/R/GAlignmentPairs-class.R GenomicAlignments/R/GAlignments-class.R GenomicAlignments/R/GAlignmentsList-class.R GenomicAlignments/R/GappedReads-class.R GenomicAlignments/R/OverlapEncodings-class.R GenomicAlignments/R/cigar-utils.R GenomicAlignments/R/coordinate-mapping-methods.R GenomicAlignments/R/coverage-methods.R GenomicAlignments/R/encodeOverlaps-methods.R GenomicAlignments/R/findCompatibleOverlaps-methods.R GenomicAlignments/R/findMateAlignment.R GenomicAlignments/R/findOverlaps-methods.R GenomicAlignments/R/findSpliceOverlaps-methods.R GenomicAlignments/R/intra-range-methods.R GenomicAlignments/R/junctions-methods.R GenomicAlignments/R/pileLettersAt.R GenomicAlignments/R/readGAlignments.R GenomicAlignments/R/sequenceLayer.R GenomicAlignments/R/setops-methods.R GenomicAlignments/R/stackStringsFromBam.R GenomicAlignments/R/summarizeOverlaps-methods.R GenomicAlignments/R/zzz.R
GenomicAlignments/build
GenomicAlignments/build/vignette.rds
GenomicAlignments/inst
GenomicAlignments/inst/CITATION
GenomicAlignments/inst/doc
GenomicAlignments/inst/doc/GenomicAlignmentsIntroduction.R
GenomicAlignments/inst/doc/GenomicAlignmentsIntroduction.Rnw
GenomicAlignments/inst/doc/GenomicAlignmentsIntroduction.pdf
GenomicAlignments/inst/doc/OverlapEncodings.R
GenomicAlignments/inst/doc/OverlapEncodings.Rnw
GenomicAlignments/inst/doc/OverlapEncodings.pdf
GenomicAlignments/inst/doc/WorkingWithAlignedNucleotides.R
GenomicAlignments/inst/doc/WorkingWithAlignedNucleotides.Rnw
GenomicAlignments/inst/doc/WorkingWithAlignedNucleotides.pdf
GenomicAlignments/inst/doc/summarizeOverlaps.R
GenomicAlignments/inst/doc/summarizeOverlaps.Rnw
GenomicAlignments/inst/doc/summarizeOverlaps.pdf
GenomicAlignments/inst/extdata
GenomicAlignments/inst/extdata/sm_treated1.bam
GenomicAlignments/inst/extdata/sm_untreated1.bam
GenomicAlignments/inst/unitTests
GenomicAlignments/inst/unitTests/test_GAlignments-class.R
GenomicAlignments/inst/unitTests/test_GAlignmentsList-class.R
GenomicAlignments/inst/unitTests/test_cigar-utils.R
GenomicAlignments/inst/unitTests/test_coordinate-mapping-methods.R
GenomicAlignments/inst/unitTests/test_findSpliceOverlaps-methods.R
GenomicAlignments/inst/unitTests/test_intra-range-methods.R
GenomicAlignments/inst/unitTests/test_readGAlignmentPairs.R
GenomicAlignments/inst/unitTests/test_readGAlignments.R
GenomicAlignments/inst/unitTests/test_readGAlignmentsList.R
GenomicAlignments/inst/unitTests/test_summarizeOverlaps-methods.R
GenomicAlignments/man
GenomicAlignments/man/GAlignmentPairs-class.Rd GenomicAlignments/man/GAlignments-class.Rd GenomicAlignments/man/GAlignmentsList-class.Rd GenomicAlignments/man/GappedReads-class.Rd GenomicAlignments/man/OverlapEncodings-class.Rd GenomicAlignments/man/cigar-utils.Rd GenomicAlignments/man/coordinate-mapping-methods.Rd GenomicAlignments/man/coverage-methods.Rd GenomicAlignments/man/encodeOverlaps-methods.Rd GenomicAlignments/man/findCompatibleOverlaps-methods.Rd GenomicAlignments/man/findMateAlignment.Rd GenomicAlignments/man/findOverlaps-methods.Rd GenomicAlignments/man/findSpliceOverlaps-methods.Rd GenomicAlignments/man/intra-range-methods.Rd GenomicAlignments/man/junctions-methods.Rd GenomicAlignments/man/pileLettersAt.Rd GenomicAlignments/man/readGAlignments.Rd GenomicAlignments/man/sequenceLayer.Rd GenomicAlignments/man/setops-methods.Rd GenomicAlignments/man/stackStringsFromBam.Rd GenomicAlignments/man/summarizeOverlaps-methods.Rd
GenomicAlignments/src
GenomicAlignments/src/GenomicAlignments.h
GenomicAlignments/src/IRanges_stubs.c
GenomicAlignments/src/R_init_GenomicAlignments.c
GenomicAlignments/src/S4Vectors_stubs.c
GenomicAlignments/src/cigar_utils.c
GenomicAlignments/src/coordinate_mapping_methods.c
GenomicAlignments/src/encodeOverlaps_methods.c
GenomicAlignments/tests
GenomicAlignments/tests/run_unitTests.R
GenomicAlignments/vignettes
GenomicAlignments/vignettes/GenomicAlignmentsIntroduction.Rnw
GenomicAlignments/vignettes/OverlapEncodings.Rnw
GenomicAlignments/vignettes/WorkingWithAlignedNucleotides.Rnw
GenomicAlignments/vignettes/precomputed_results
GenomicAlignments/vignettes/precomputed_results/U1.sbcompHITSa.rda
GenomicAlignments/vignettes/precomputed_results/U1.sbcompHITSb.rda
GenomicAlignments/vignettes/precomputed_results/exbytx.rda
GenomicAlignments/vignettes/summarizeOverlaps-modes.pdf
GenomicAlignments/vignettes/summarizeOverlaps.Rnw

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