Files in Bioconductor/GenomicAlignments

Representation and manipulation of short genomic alignments

DESCRIPTION

NAMESPACE

NEWS

R/GAlignmentPairs-class.R R/GAlignments-class.R R/GAlignmentsList-class.R R/GappedReads-class.R R/OverlapEncodings-class.R R/cigar-utils.R R/coordinate-mapping-methods.R R/coverage-methods.R R/encodeOverlaps-methods.R R/findCompatibleOverlaps-methods.R R/findMateAlignment.R R/findOverlaps-methods.R R/findSpliceOverlaps-methods.R R/intra-range-methods.R R/junctions-methods.R R/pileLettersAt.R R/readGAlignments.R R/sequenceLayer.R R/setops-methods.R R/stackStringsFromGAlignments.R R/summarizeOverlaps-methods.R R/utils.R R/zzz.R README.md

inst/CITATION

inst/extdata/sm_treated1.bam

inst/extdata/sm_untreated1.bam

inst/unitTests/test_GAlignments-class.R inst/unitTests/test_GAlignmentsList-class.R inst/unitTests/test_cigar-utils.R inst/unitTests/test_coordinate-mapping-methods.R inst/unitTests/test_findSpliceOverlaps-methods.R inst/unitTests/test_intra-range-methods.R inst/unitTests/test_readGAlignmentPairs.R inst/unitTests/test_readGAlignments.R inst/unitTests/test_readGAlignmentsList.R inst/unitTests/test_summarizeOverlaps-methods.R man/GAlignmentPairs-class.Rd man/GAlignments-class.Rd man/GAlignmentsList-class.Rd man/GappedReads-class.Rd man/OverlapEncodings-class.Rd man/cigar-utils.Rd man/coordinate-mapping-methods.Rd man/coverage-methods.Rd man/encodeOverlaps-methods.Rd man/findCompatibleOverlaps-methods.Rd man/findMateAlignment.Rd man/findOverlaps-methods.Rd man/findSpliceOverlaps-methods.Rd man/intra-range-methods.Rd man/junctions-methods.Rd man/pileLettersAt.Rd man/readGAlignments.Rd man/sequenceLayer.Rd man/setops-methods.Rd man/stackStringsFromGAlignments.Rd man/summarizeOverlaps-methods.Rd

src/GenomicAlignments.h

src/IRanges_stubs.c

src/R_init_GenomicAlignments.c

src/S4Vectors_stubs.c

src/cigar_utils.c

src/coordinate_mapping_methods.c

src/encodeOverlaps_methods.c

tests/run_unitTests.R

vignettes/GenomicAlignmentsIntroduction.Rnw

vignettes/OverlapEncodings.Rnw

vignettes/WorkingWithAlignedNucleotides.Rmd

vignettes/precomputed_results/U1.sbcompHITSa.rda

vignettes/precomputed_results/U1.sbcompHITSb.rda

vignettes/precomputed_results/exbytx.rda

vignettes/summarizeOverlaps-modes.pdf

vignettes/summarizeOverlaps.Rnw

Bioconductor/GenomicAlignments documentation built on March 28, 2024, 9:59 a.m.