Files in PapenfussLab/StructuralVariantAnnotation
Variant annotations for structural variants
.Rbuildignore
.gitignore
.travis.yml
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/BreakpointGRanges.R
R/StructuralVariantAnnotation.R
R/eventDetection.R
R/extensions-VCF.R
R/plotting.R
R/unittesthelper.R
R/util.R
R/vcfConstants.R
README.md
StructuralVariantAnnotation.Rproj
figures/Overview.ai
inst/extdata/COLO829.10X.longranger.largeSVs.vcf
inst/extdata/COLO829.nanopore.sniffles.vcf
inst/extdata/COLO829T.purple.sv.ann.vcf.gz
inst/extdata/MT.vcf
inst/extdata/breakdancer-1.4.5.vcf
inst/extdata/breakend.vcf
inst/extdata/colo829_nanoSV_truth_overlap.vcf
inst/extdata/colo829_somatic_gridss.vcf.gz
inst/extdata/colo829_somatic_manta.vcf
inst/extdata/colo829_somatic_novobreak.vcf
inst/extdata/crest.vcf
inst/extdata/delly-0.6.8.vcf
inst/extdata/gridss-missingPartner.vcf
inst/extdata/gridss-na12878.vcf
inst/extdata/gridss.bedpe
inst/extdata/gridss.vcf
inst/extdata/manta-0.29.6.vcf
inst/extdata/manta-1.1.1.vcf
inst/extdata/multipleAltSVs.vcf
inst/extdata/na12878_chr22_Sudmunt2015.vcf
inst/extdata/na12878_chr22_crest.vcf
inst/extdata/na12878_chr22_hydra.vcf
inst/extdata/pindel-0.2.5b6.vcf
inst/extdata/representations.vcf
inst/extdata/simple.vcf
inst/extdata/tigra-0.3.7.vcf
inst/extdata/truthset_somaticSVs_COLO829.vcf
inst/extdata/unnamed.bedpe
inst/extdata/vcf4.2.example.sv.vcf
man/StructuralVariantAnnotation.Rd
man/align_breakpoints.Rd
man/breakendRanges.Rd
man/breakpointGRangesToVCF.Rd
man/breakpointRanges.Rd
man/breakpointgr2bedpe.Rd
man/calculateReferenceHomology.Rd
man/countBreakpointOverlaps.Rd
man/elementExtract.Rd
man/extractBreakpointSequence.Rd
man/extractReferenceSequence.Rd
man/findBreakpointOverlaps.Rd
man/findInsDupOverlaps.Rd
man/findTransitiveCalls.Rd
man/hasPartner.Rd
man/isStructural.Rd
man/isSymbolic.Rd
man/numtDetect.Rd
man/pairs2breakpointgr.Rd
man/partner.Rd
man/rtDetect.Rd
man/simpleEventLength.Rd
man/simpleEventType.Rd
tests/testthat.R
tests/testthat/test-BreakpointGRanges.R
tests/testthat/test-extensions-VCF.R
tests/testthat/test-plotting.R
tests/testthat/test-util.R
vignettes/vignettes.Rmd
