Files in GenomicAlignments

Representation and manipulation of short genomic alignments

README.md

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

src/coordinate_mapping_methods.c

src/encodeOverlaps_methods.c

src/GenomicAlignments.h

src/S4Vectors_stubs.c

src/IRanges_stubs.c

src/R_init_GenomicAlignments.c

src/cigar_utils.c

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

vignettes/summarizeOverlaps.Rnw

vignettes/WorkingWithAlignedNucleotides.Rnw

vignettes/GenomicAlignmentsIntroduction.Rnw

vignettes/OverlapEncodings.Rnw

vignettes/summarizeOverlaps-modes.pdf

vignettes/precomputed_results/U1.sbcompHITSa.rda

vignettes/precomputed_results/U1.sbcompHITSb.rda

vignettes/precomputed_results/exbytx.rda

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

inst/CITATION

inst/doc/summarizeOverlaps.R

inst/doc/summarizeOverlaps.Rnw

inst/doc/summarizeOverlaps.pdf inst/doc/GenomicAlignmentsIntroduction.R inst/doc/GenomicAlignmentsIntroduction.pdf inst/doc/WorkingWithAlignedNucleotides.R inst/doc/WorkingWithAlignedNucleotides.pdf

inst/doc/WorkingWithAlignedNucleotides.Rnw

inst/doc/GenomicAlignmentsIntroduction.Rnw

inst/doc/OverlapEncodings.Rnw

inst/doc/OverlapEncodings.R inst/doc/OverlapEncodings.pdf

inst/extdata/sm_untreated1.bam

inst/extdata/sm_treated1.bam

inst/unitTests/test_coordinate-mapping-methods.R inst/unitTests/test_intra-range-methods.R inst/unitTests/test_GAlignments-class.R inst/unitTests/test_findSpliceOverlaps-methods.R inst/unitTests/test_summarizeOverlaps-methods.R inst/unitTests/test_GAlignmentsList-class.R inst/unitTests/test_readGAlignments.R inst/unitTests/test_cigar-utils.R inst/unitTests/test_readGAlignmentPairs.R inst/unitTests/test_readGAlignmentsList.R

GenomicAlignments documentation built on Nov. 8, 2020, 8:12 p.m.