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.

Author
Hervé Pagès, Valerie Obenchain, Martin Morgan
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.10.0

View on Bioconductor

Man pages

cigar-utils
CIGAR utility functions
coordinate-mapping-methods
Map range coordinates between reads and genome space using...
coverage-methods
Coverage of a GAlignments, GAlignmentPairs, or...
encodeOverlaps-methods
Encode the overlaps between RNA-seq reads and the transcripts...
findCompatibleOverlaps-methods
Finding hits between reads and transcripts that are...
findMateAlignment
Pairing the elements of a GAlignments object
findOverlaps-methods
Finding overlapping genomic alignments
findSpliceOverlaps-methods
Classify ranges (reads) as compatible with existing genomic...
GAlignmentPairs-class
GAlignmentPairs objects
GAlignments-class
GAlignments objects
GAlignmentsList-class
GAlignmentsList objects
GappedReads-class
(Legacy) GappedReads objects
intra-range-methods
Intra range transformations of a GAlignments or...
junctions-methods
Extract junctions from genomic alignments
OverlapEncodings-class
OverlapEncodings objects
pileLettersAt
Pile the letters of a set of aligned reads on top of a set of...
readGAlignments
Reading genomic alignments from a file
sequenceLayer
Lay read sequences alongside the reference space, using their...
setops-methods
Set operations on GAlignments objects
stackStringsFromBam
Stack the read sequences stored in a BAM file on a region of...
summarizeOverlaps-methods
Perform overlap queries between reads and genomic features

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